As for the Minor Arcana, I will mention the qualities of the suits:
Swords: air, intellect, debate, nobility/military
Wands: fire, energy, ambition, creativity
Cups: water, emotion, faith, love
Pentacles: earth, body, possessions, wealth
Aces represent each suit in its quintessential form. The court cards are self-explanatory.
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From this, hopefully you can see the logic behind all the choices I made. I strove for some amount of moral balance -- Janus as page of cups makes that suit a little darker, while Masa & Mune bring a positive note to Swords. I debated a bit over Queen of Swords and Queen of Wands, but the correct choices became clear: the power and ambition of Queen Zeal fits Wands; the militancy, logic, and persuasiveness of Mother Brain fits Swords.
I also debated over the placement of Ozzie -- does his greater importance to the story, and his dynasty, warrant King placement or not? Eventually I decided to assign him as Knight of Pentacles. This way, each of the Mystical Knights gets a Knight card, and King Guardia XXI can be King of Pentacles. I believe King Guardia XXI's placement is correct due to his overall qualities and possession of the Rainbow Shell (the Ace of Pentacles). While Yakra/Chancellor was removed, he could still be used in the suit cards (update: now he is, on 7 of swords).
As for the Knight of Cups, Toma seems like the best choice, but the drawback is that all Cups royals would be from 600 ad. One of my ideas is equitable representation of the different time periods, especially prehistory and future, so that would be the main argument for Kino or Doan. With that said, I still lean towards Toma.
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for the suits, I sought matches that also provided varied representation and logical connections. as always, the matches must be made with the meanings, rather than surface similarity, e.g. 5 of pentacles may resemble Manoria Cathedral, but it's a much better fit for a ruined future dome or Algetty. I also tried to maintain the theme of including 'full sets' (e.g. 3 gurus and 7 party members); this helped me decide on Zeal Palace for 5 of swords, Kajar for 9 of pentacles, Enhasa for 7 of Cups, and Blackbird for 8 of wands. this way, all major Zeal locations are included, and each with their own suit which fits their character (in addition, blue pyramid is 2 of wands). Additionally, I tried to create logical links between the cards where possible. For example, 3 of pentacles is Fiona's Shrine, while 3 of cups is the campsite afterwards. better yet, 5 of swords is the Masa & Mune fight, while 6 of swords is winning the hilt. Then of course there's representation of time periods, significant locations, and characters. While assigning Mud Imp & red/blue beasts to 2 of pentacles is not one of my stronger connections, it does represent the Algetty/Mt. Woe region. Various dungeons would fit 7 of pentacles, but it's important that Black Omen gets a slot. 7 of swords could fit a few different things (eg Kino stealing the Gate Key), but Yakra/Chancellor is most deserving.
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Here I'll discuss the Suits in further detail:
2 of Swords: Magus at North Cape, fight or join? (cf 8 of cups). A conflict between two different sides, a decision that must be made, a situation that calls for discipline and introspection. There aren't many forks in CT, but this is one of them. You must decide to either settle the score with Magus, or let him join; there are rationales for each path, yet you must choose decisively and accept the consequences. The situation also fits the suit of swords.
3 of Swords: Atropos XR (confrontation or aftermath could work). A card of heartbreak, sorrow, of painful truths coming out. The situation between Robo & Atropos fits well here: betrayal, returning Atropos to her senses, and the tragedy of being unable to save her.
4 of Swords: End of Time. A card of rest and repose, recovering from battle, meditation. The End of Time serves well here, as a quiet place for the party to rest from their adventure and plan their next move. In a playthrough, the first visit to the end of time is a great stopping place after the madness of breaking out of jail and seeing the ruined future.
5 of Swords: captured in Zeal Palace. The themes are defeat, overconfidence, biting off more than you can chew. One of the few times the party is defeated is in the Zeal throne room, confidently challenging these powerful magic-users, only to be overwhelmed by the Golem (and that physical attack with orange shots is dangerous!). And Zeal Palace itself is characterized by hubris.
6 of Swords: opening the passage to Magus' Castle. a breakthrough, moving away from troubles, solving problems and making progress. Frog has finally stopped moping around and has taken the initiative, cleaving through the cliffside and opening the way to Magus. While you've made a breakthrough, there's still plenty of challenges ahead; Magus' castle awaits, but now you're on the way and ready to take it on.
7 of Swords: Yakra/Chancellor. The thief card, it refers to stealth, diplomacy, getting your way indirectly through deceit or persuasion, or guarding against such intrigue. There are a few different situations that would fit here, such as Kino stealing the gate key, or recovering your equipment on the Blackbird. However, Yakra/Chancellor is the most notable deceiver in CT -- the first Yakra kidnapped the Queen, and his descendant went all out, prosecuting you in a kangaroo court, lying to Marle, and framing the King. as despicable as he is, he's an important character, and should be represented here.
8 of Swords: standing trial (the stained-glass depiction of justice should serve well here). the theme is "damned if you do, damned if you don't", you're ensnared in a situation where you're being accused and censored, anything you say can be used against you, but you must persevere and act anyway. there could not be a better analogy to the Trial.
9 of Swords: Ocean Palace (Schala turning up the Mammon Machine?). nightmares, anxiety, mental anguish, negativity. this was a tricky one to assign, and the Red Gate would fit here. however, I chose the Ocean Palace, as it's a tense situation leading to calamity, with Schala experiencing turmoil as she turns up the Mammon Machine. there's also a sense of waking up from a bad dream, and the unsustainable hubris of Zeal will soon come to an end. likewise, while the worst will come to pass for the party, it turns out that the situation is still salvable. not a perfect analogy, but it works, it provides representation for the Ocean Palace, and segues into the next card...
10 of Swords: Chrono's death (Lavos' blast as swords). a nadir, despair, unavoidable disaster, the worst is over. Chrono's death fits thematically and aesthetically. while this is a very low point, there's still hope for recovery, as eventually proven by the game's namesake.
2 of Wands: choosing an artifact from the Blue Pyramid. a choice to be made between two viable alternatives. not as conflicted as 2 of swords, both choices are beneficial, but you have to settle on one. the best CT analogue I can think of is the Blue Pyramid -- both the Swallow and Safe Helm are excellent pieces of equipment, but you can only take one or the other. do you want a swift attack, or stalwart defense?
3 of Wands: learning magic from Spekkio. a strong start, getting positive returns, opportunities, a favorable exchange, but it's only the beginning. learning magic is a major step forward, the beginning of using much more powerful techs, which fits.
4 of Wands: rescuing Queen Leene/Marle in 600 ad. the foundation is in place, the first stage is now complete, but there's much more ahead. this is in parallel to completing the first quest in 600 ad -- it's an important victory, but it's only an introduction to what lies ahead.
5 of Wands: fighting Masa & Mune. serious competition, a contest or battle to test your mettle. Masa & Mune fight you to test your worthiness, and this is the first time you'll hear boss battle 2. you've fought bosses before, but now it's getting more serious, which reflects 5 of wands. there's also a nice parallel with the number of combatants -- the party and masa & mune in separate forms makes 5.
6 of Wands: winning the Masamune hilt. victory, an exchange of energy between the crowd and the champion. likewise, you've triumphed over Masa&Mune and attained the honor of possessing the hilt, while Grandleon for its part has found a worthy wielder. It also follows logically after 5.
7 of Wands: Battle of Zenan Bridge. under siege, standing your ground, perseverance; you're on the defensive, but you can fend off the opposition. the Battle of Zenan Bridge seems to fit best here: you hold off the Mystic invasion, and Ozzie doesn't seem to expect such resistance.
8 of Wands: Blackbird. swiftness, efficiency, events happening quickly, controlling energy to get the most out of it. the Blackbird is an engineering marvel by all accounts, capable of flying swiftly and gracefully. not only that, but this chapter consists of rapid events: getting captured, the Epoch gaining wings, defeating Dalton once and for all. I think it's important to represent the Blackbird, and other possibilities (time gate, epoch) are already trumps.
9 of Wands: climbing Death Peak. weary yet determined, you're on the home stretch, a little more effort will get you there. likewise, saving Chrono is an arduous process, and Death Peak is particularly challenging, but in spite of it all, nothing will keep you from the summit.
10 of Wands: the Chef (600 ad). overburdened, expending too much energy, losing sight of what's important. I had to scrape for this one, but the chef fits. he puts out alot of energy in running the kitchens, too much in fact. it takes the party to remind him of greater priorities, like helping his bro the knight captain.
2 of Cups: Chrono & Marle (meeting under Leene's Bell, NOT Death Peak (reserved for Lovers)). partnership, romance, the beginning of a relationship. this is the minor arcana equivalent of the Lovers, although there are different nuances; this card has more of a sense of initial meetings, as opposed to the decision and commitment of the Lovers. likewise, Chrono bumping into Marle under Leene's Bell is the beginning of their relationship, just as their reunion on Death Peak cements it. I thought the best way to handle the similarities and differences here is to assign Chrono & Marle to both, but differentiated by the two events.
3 of Cups: Campsite (post Fiona's sidequest). celebration, gatherings, abundance, emotional bonds. this fits the camp scene, with the party all together and discussing larger concepts. there's a strong sense of companionship, and also of celebration, since you've completed the sidequest and changed desert to forest.
4 of Cups: Frog's burrow. dissatisfaction, boredom, stagnation, being stuck in a rut. at this point, Frog has retreated from the world, staying in his burrow because he lacks the will and confidence to continue the quest. this fits the sense of stagnation and being stuck. while rest can be positive, this card is for when you're restless and not progressing.
5 of Cups: flashback to Glenn's defeat, after being transformed into Frog. setbacks, regret, loss, focusing only on the negative. this fits well with Frog's disastrous encounter with Magus. it seems like all is lost, even his human form, and it haunts him after. but just as in the card, all is not lost, and it's easy to lose sight of the remaining positives and the potential to pull through.
6 of Cups: Leene's Bell. reminiscence, nostalgia, the familiar, good things from the past. this was a tricky association, but I think Leene's Bell fits. its ringing marks the beginning, middle, and end of the game, serving as a memento to how far you've come, and how it all began while having fun at a fair.
7 of Cups: Enhasa. daydreams, fantasy, visions, aspirations, delusions. this is about creativity and dreams, which can sometimes run wild. what better connection than the city of dreams, Enhasa? not to mention the other references to the locations of Zeal within the suits.
8 of Cups: Magus joins at North Cape (cf 2 of swords). change in lifestyle, leaving things behind, striking out on a new path. your old life is not satisfactory, so you make a bold decision and embrace the new. likewise, Magus has spent the game seeking to battle Lavos on his own terms, 1 to 1, and generally regarding the party as an obstacle. in fact, he sees most individuals as either useful pawns or as enemies to be defeated. for Magus to join the party, even to take down a common foe, is a huge change. this fits the theme of abandoning one's old lifestyle to embrace the new and unknown.
9 of Cups: Medina Village post Ozzie's Fort. fulfillment, emotional satisfaction, happiness. I was a little unsure about this one, especially since there's more emphasis on individual happiness rather than communal. however, it's safe to say that when you change Medina Village for the better, there is a sense of emotional fulfillment -- the Mystics are no longer harboring a grudge towards humans, their society is run more fairly, life is happier for them overall. if you can come up with a better alternative, by all means let me know, but keep in mind that as a cups card, this is about emotional wealth rather than material.
10 of Cups: Moonlight Parade. abundance, achievement, shared happiness. this is 9 of cups +1, with a sense of lasting, communal well-being. there's also a sense of achieving a long-term goal, which makes it a perfect association with the moonlight parade -- a communal celebration to top off your (and the Planet's) victory over Lavos.
2 of Pentacles: red/blue beasts and mud imp. a balancing act, juggling, a precarious status quo that could easily be toppled. the Mud Imp's control of two equal and opposite beasts who are stronger than he is fits here. in a larger sense, it fits with the dungeon he's guarding, Mt. Woe, a chained floating mountain that is maintained only through the magic of Zeal. I wasn't sure about this one at first, but the additional parallel with Mt Woe confirms my choice. it also provides some representation to the Algetty/Mt. Woe region, easily overlooked in favor of Zeal, but in many ways just as significant.
3 of Pentacles: Fiona's Shrine? Manoria Cathedral? something else?. mastery, achievement, craftsmanship, bringing to fruition. likewise, Fiona's forest and shrine are accomplished through the decision and efforts of the party, and especially through Robo's commitment. there's also an aesthetic parallel with the shrine.
4 of Pentacles: Porre Mayor. material possessions, security, wealth, even hoarding and miserliness. the mayor of Porre is certainly secure in his wealth and status, but he also embodies the negative aspects of the card, at least until the party corrects his ways. it's also fitting that the Ace of Pentacles, the Rainbow Shell comes into his possession.
5 of Pentacles: Ruined Future Dome (or Algetty). poverty, hard times, out in the cold. the people huddled in ruined domes in the future, and the earthbound ones living in their caves far below the splendor of Zeal, both fit very well. I lean towards the future for two reasons: Algetty has a bit of representation in 2 of pentacles, and the future offers good opportunity for illustration, particularly the sealed doors (as an aside, the rider-waite illustration is one of my favorites)
6 of Pentacles: saving Fritz (repairing Robo?). generosity, charity, freely giving and taking. an important concept here is that assistance is offered willingly, no strings attached, and this positive karma can come back to you. likewise, rescuing Fritz from a wrongful execution leads to great discounts & service at the shop. repairing Robo would also fit here, since he contributes quite a bit in return for your help. however, Robo is represented elsewhere, unlike Fritz.
7 of Pentacles: progressing through the Black Omen. perseverance, patience, working towards long-term goals. success is on the horizon, but there are many obstacles along the way, and it'll take a slog to get there. likewise, the Black Omen is the longest dungeon in the game, it's full of robots, mutants, and aliens, but it's also full of useful stuff, and Lavos awaits at the end. other dungeons could fit here, like Mt. Woe or Denadoro, but the Black Omen is best; I also think it's important to assign the Black Omen somewhere, given its fairly significant presence.
8 of Pentacles: repairing the Masamune w/ Dreamstone (Melchior). apprenticing, craftsmanship, skillful and creative work. this is about applying yourself to a field, taking on a new project or commission, with strong potential. likewise, the party has retrieved Dreamstone, and Melchior has set to work on the Masamune/Grandleon. this is a new, ambitious task, probably the best endeavor he's taken on in 1000 ad. there's definite progress being made, which fits.
9 of Pentacles: Kajar. abundance, material wealth, financial security. this card is about having plenty, but in a material and somewhat private sense. in Zeal, the three main locations are the seat of government and magical power, the center of magical research and experimentation, and the abode of dreams. Kajar is a place of luxury, and of concrete, tangible work in magic, which makes for a good fit. of course, the abundance here is not shared with those living on the surface below, which again parallels the limited, private nature of this card as compared to the 10 of pentacles.
10 of Pentacles: Millennial Fair, ft Melchior and the woman. prosperity, fortune, inheritance, relations. This card builds on the previous; the wealth is now being shared for the benefit of all. likewise, Guardia is stable and prosperous, so that it can celebrate its thousandth year by bringing trade and entertainment to the people. there's also a sense of relationships here, and this is where Chrono & Marle first meet. finally, the illustration really lends itself to the Millennial Fair, and the rich elder could easily be Melchior selling his weapons, with the woman and other characters nearby.