Yeah that would be interesting. Also events would focus on Zeal, I would allow characters that come outside of it because that would be one tiny planet if that was the only continent XD.
I've always taken the maps in Chrono Trigger to be representative rather than literal. I would say that there were other sky-islands besides those seen in the game; however, they weren't visited because they simply weren't relevant to the plot.
The different casting classes could represent different styles of magic. For example, you may be a bookish wizard who practices through having a wide variety and a better understanding of magic, or you could be a sorcerer who specializes more in magic, has less of an idea what they are doing and uses force of will for casting; or a bard who uses magic more as an art form and draws magic from the arts. You could also have artificers who represent more hard-nosed scientist/researcher types like Belthasar and the people of Kajar.
It would be harder to fit in druids, clerics, and paladins. Not sure how they would fit in, but I could see some among the Earthbound, perhaps some have discovered a type of magic that only comes from attunment to the natural world or some other force.
The game only showed us the final days of Zeal. We're told that it had previously focused on elemental magic, but the discovery of Lavos caused the entire culture to shift gears. By setting the campaign prior to that, you'd presumably have a society more akin to that of the Dragonians, who revered the elements and seemed to worship the planet itself as a divinity. That could be the basis for the divine caster classes.
I like the idea of seeing Zeal through the eyes of more "common people" rather than royalty. There are a number of interesting scenarios I can think of:
-Some of your party members are Enlightened Ones stranded somehow on the surface. The weather and cold make it difficult to even cast spells, and your only hope back home is to band with some Earthbound Ones. However casting aside such prejudices are not going to happen overnight. Furthermore one or more of your Enlightened One party members has the ability to sense if someone has magic-and you find that even among the Earthbound Ones there is evidence of perhaps some...activity between the two groups-or it could be that just as some people can be born without magic on the floating islands, so too can some Earthbound Ones just have the potential for magic.
An NPC mentions that "Long ago, the Enlightened Ones and the Earthbound Ones lived as one." This could be taken to mean a time before contact with the Frozen Flame, but I prefer to interpret it as sometime after the founding of Zeal but before the present day. The campaign could be set during such a time, with a definite social stratification of magical haves and have-nots, but without the severe classism shown in the game.
Also, the dichotomy might not have been as extreme in earlier times. The genetics for magical talent may have not yet died out among the Earthbound Ones. If the ability is carried in a recessive gene, it might pop up among families who haven't produced a magician for many generations. Enlightened Ones would be spellcasters more often than not, just as Earthbound Ones would mostly be nonspellcasters, but there could be some crossover.
In any event, adventurers in most campaign settings are seen as distasteful by the upper class; a necessary evil (regardless of the adventurers' actual alignment) to accomplish unsavory tasks. For that reason, an Enlightened adventurer might be viewed as barely above an Earthbound One by those who would otherwise be his social equals.
-Researchers begin to be concerned about how all the spells that make the floating islands rise and be habitable are taking a huge drain from the sunstone. Your party members are on an expedition to search for other sources of energy-hopefully another sunstone. Bonus if your party finds out there is no other sunstone and everyone has to come up with a solution.
There are 65 million years unaccounted for in the canon, with 3 million of those allowing for the existence of magic. That makes for a lot of ancient ruins to delve for any number of reasons. You could rework just about any published module to fit into that context.
-Extending the one above, Lavos is discovered, now your party members have to deal with the issue, support or think the nation is heading the wrong direction? Your party members may be dissenters, and each goes missing one by one, and you have to rescue one another and help stop the madness that is encroaching on Zeal.
-Mirroring Netheril, instead of the whole Lavos thing, Zeal is threatened to fall due to some jerk ass mages trying to attain godhood and take power from a god of magic-and succeed which actually ends up killing the deity and depriving the world of magic.
These two pretty much describe Zeal's final days as portrayed in the game.
The PCs could be followers of the Gurus, and are banished along with them.
Lavos could be seen as a god of magic, since the Frozen Flame was responsible for humans' magical aptitude. Except instead of being killed, Lavos destroys the ones attempting to steal its power. Magic doesn't die, but most of its practitioners do, which has much the same effect.
Just curious, how would you class the cast of CT? 
I wouldn't try to duplicate all their abilities one-for-one, as some are just too bizarre to explain; how does a nonmagical Ayla summon a giant dinosaur tail outside her own era? But with the house rules I suggested, here's how I'd do it. Where specific techs aren't mentioned, I feel they can be adequately represented by the given class's existing abilities or feats which are similar in function (Crono's Cyclone is Whirlwind Attack, for example).
Crono: Fighter with Weapon Focus and Weapon Specialization in katana. (In this setting, I would consider the katana to be a martial weapon rather than exotic.) Unique feats that allow him to cast
lightning bolt, chain lightning, sunburst, and
raise dead (Lightning, Lightning 2, Luminaire, and Life, respectively).
Barring unique feats, I'd have him as a fighter/sorcerer and just select electricity- and light-based spells.
Marle: Cleric of a nonspecific deity, with the healing and water domains. Unique feat that allows her to cast
haste.
Lucca: Wizard (evoker) specialized in fire spells. Her guns would be reflavored crossbows.
Lucca might be better represented as an artificer, but I'm not familiar with that class since I didn't really care for Eberron's mechanics (absolutely loved the geopolitical setup though).
Frog: Paladin with his smite attacks reflavored as water spells and usable against nonevil foes. Frog Squash is one of those bizarre abilities I wouldn't try to replicate.
Robo: Warforged (yeah, Eberron) fighter with Improved Unarmed Strike, and Weapon Focus and Weapon Specialization in unarmed strike. Unique feats that allow him to
cast mass cure light wounds, mass cure moderate wounds, chain lightning, fireball, and
call lightning (Cure Beam, Heal Beam, Laser Spin, Area Bomb, and Shock, respectively).
Barring unique feats... I don't even know. A fighter/druid maybe? Robo's abilities are a real grab bag of odd stuff when translated to D&D equivalents.
Ayla: Monk with a unique feat that allows her to cast
Charm Monster.
Magus: Wizard with Spell Focus and Greater Spell Focus in evocation, and Exotic Weapon Proficiency in scythe. (The scythe is normally a martial weapon, but doing it this way prevents the need to give him both Simple and Martial Weapon Proficiency.)
