Interesting topic, many of these can overlap though. I'll start with the main cast.
Sora: (FFVI) Locke~Both seek adventure, have females they care about, can be childish, goofy, fun loving but also have a serious side that comes out when need be.
Riku: (FFIV) Cecil Harvey/Kain~When it comes to Cecil, both use to work for bad guy or did really bad things, went over to the light side and are both changed men. When it comes to Kain, the jealousy aspect.
Kairi: (FFIV) Rosa~Love interest who don't do much but be support for the male lead, get kidnapped, poisoned, stolen heart, killed, however you look at it. Both are sweet and caring people and play big support roles for the heroes be it POH or powerful White Mage.
Axel/Lea: (FFIX) Zidane/Gilgamesh~While Axel isn't a woman chaser, both are charismatic, fun, joke around with both their friends and enemies. Both don't always make the right choices but their hearts are in the right place. Axel's like Gilgamesh for almost similar reasons of being comic relief too.
Roxas: (VI) Terra Brandford/Beatrix (FFIX)~Both Roxas and Terra don't really know how the world work and their creations were not what you would call natural. Both taken by a evil force at birth and do task under their name. And both find new lives once they leave, with both old and new friends at their side. Roxas is like Beatrix in that they both start to realize what they are doing is wrong, but are unsure to leave their leader. Also both Beatrix and Roxas are uber powerful.
Xion: (FFIX) Vivi/Yuna (FFX)~Xion and Vivi are both born as puppets who get caught up in plots far bigger then them. They both question their existence, grow from them, and become greater characters then their original creations intended them to be. They are both one of a kind in their worlds. Xion's like Yuna because she's fully prepared to die for her cause and love ones without hesitation.
Terra: (FFIX) Steiner~Both powerful and strong warriors who are idiots. They follow someone who is clearly evil. But because of how they were raised/trained they respect/honor who they serve. Eventually they come to terms with who they served and what they've done, and become better people afterwords.
Aqua: (FFVI) Celes/Tifa (FFVI)~I literally thought of the Celes jail beat down when Terra and Ven verbally attacked her in Radiant Garden. Both Aqua and Celes are strong magic user fighters and were put in situations where suicide might have been the only way out. Aqua and Tifa both are like the moms/big sisters of their group. I guess Aqua can relate to any FF big sister figure.
Ventus: (FFX) Tidus~I didn't just want to copy Sora's list. Both Ventus and Tidus are supportive, loud, immature, good natured, curious, and want to help those they care about. Both also come from different worlds from their friends and have ties to big evils. Darkness and Sin respectively.