Hmmm...alright I guess...
1. Magus - He's got a great design and we get to see him at 3 stages in his life (Janus, Maou/Prophet & then with Crono & Co.). I think he's one of the most inspiring characters as well. It's nice that you can think of him either as an unrelenting, supremely focused spirit of vengeance (OMG, FLAMING SKULL MAGUS WOULD BE SO EFFING AWESOME!!) or a driving force willing to sacrifice all to get back what he once lost. Also one of the most tragic characters (though they've really all got something)...As far as battle, he should be the most potent Magic user once you get him, and even when the others have caught up with him, he's still 4th with Dark Matter and with CTDS has a very decent physical attack as well. Plus, he's the most quotable.
Dammit, I just have a hard time ranking them because all of them between Magus & Marle kick ass...>_< Okay, no, I can do this~!!
2. Crono - Normally I too probably wouldn't rate a silent protagonist so high, but Crono is easily the best example of such. Plus, he's THE MAN in battle with the ultimate single Tech, Luminaire and a great physical tech with Confuse. Personality-wise, you can play him a couple different ways...Kind of cautious, reluctant hero (forced into things by Marle) or a guy who just does things as he sees them (& may even be an ass about it). His reactions to things is pretty neat for having to express himself mostly just through a couple sprites...but his sacrifice is key, I think and a really great scene as well.
3. Robo - I love me some robots, that's for damn sure. He plays like a sort of innocent character & is also incredibly selfless. Whether its giving up 400 years for a forest or offering up his own legs, he's always thinking of others...Plus, he's the only character that has to fight his love AND his mother (the equivalent would be for Magus to have had to fight Schala as well as Zeal). In battle, he's my go-to guy. The best party healing Tech, access to all Magic types but Water, 3rd best Magic Tech with Shock, along with Uzzi Punch makes him an all-around powerhouse...Just gotta cover up his Speed gap and low Magic Defense and this tank is ready to roll...of course, there's also CTDS's Apocalypse Arm, which gives you a new way to use him (and giving you the ability to get 9999 damage before Ayla levels enough to get the Bronze Glove)...
4. Lucca - I've got a soft spot for nerdy/dorky girls and Lucca is certainly one of those. She's the science wiz with a wacky, offbeat personality. Her present was molded by her past and her drive to protect people from technology with a heavy dose of knowledge. She also went on to be one of the key figures in CC. Flare makes her my #2 in battle and her new equip from CTDS, the Elemental Aegis, is nothing too shabby either. Plus, her alternate dimension goth, katana-wielding version is in Magness, ha!
5. Frog - I was never really a big fan of him. He just seemed to run away from his problems too much before Crono & Co. finally kicked his ass back into gear. With the retranslation though, the fact that he has an incredible sense of empathy, even as a child, shone through and made me like him better (and strengthened my resolve that it doesn't make sense for him to fight Magus on the Cape). Ever the conflicted knight character. In battle, I'd put him only above Marle. He's not as good at healing as Robo and his physical and Magic techs aren't great either...Frog Squash is only good if he's low, which means you have to have another healer on standby to sustain usage...The scenes with his flashbacks and his redemption with the help of Masa & Mune are some of the best scenes, though.
6. Ayla - A great character, don't be fooled because I put her so low. Not a lot of bi characters in RPGs made her really unique...add on the fact that she totally bitchslapped that douchey guy Kino (totally deserved it!) and gives one of the BEST SPEECHES IN RPGdom...oh, and she's a powerhouse in battle as well. Tail Spin is as powerful as Robo's Shock and counts as a kind of non-elemental Magic (though it's got iffy range)...Triple Kick is probably up there as most powerful physical Tech and she's got the highest critical hit % (though it falls once she gets Bronze Fist, that's only because it becomes a 9999 hit attack)...She's also got some good new Relic in CTDS. The one thing I don't really like about her is that Prehistory is just my least favorite era to stomp around in. She deserves more respect than she usually gets.
7. Marle - Someone has to be last. She's probably my least favorite character though she has some touching moments as much as anyone else. In battle she's easily replaced with Haste Helms...her only power lies with relying on others to help her out because Ice 2 isn't really going to be helping you out and she doesn't have any multi-targeting healing Techs, which to me makes her nigh-useless. I think CE did a wonderful job making her not suck so much (though solo-Marle stuff was BRUTAL). I don't usually enjoy these types of free-spirit Princess types, but she would probably top the list of such. The scene with her & Crono atop Death Peak (don't give me any of that "it doesn't have to be Marle" BS either) is one of the most touching in all of RPGdom.
I could easily see switching Frog & Ayla's spots, but I think Frog wins out because the long-haired human Glenn sprite was so kickass.