amok: Others, such as Ziggurat, has a choice between several characters, both male and female, but there is no customization and playing as Ozuna the Bard is very different from for example Corvus the Vampire, the choice here is purely gameplay / gamemechanics related.
Hm, tricky question whether games like that should be included or not. :/
amok: At a glance, though, I did not see Trails in the sky there, and I know the 3d at least have fixed main protagonist (Kevin Graham). (I have a feeling many of the more story driven RPG's will have a fixed protagonist, to make romance and relations to work).
I'm not sure those two aspects are actually as related as one would think. Many of the games that give you choices are still story-driven (e.g. Baldur's Gate, Mass Effect), while some others that have preset characters don't really have a good reason for that, at least concerning the story-telling (Nox should work just as well with a female main character, for example; they probaby just didn't have the resources or thought players would not be interested in that at the time; and Revenant, while having a fixed story, is mostly a combat-driven game with very rare story bits strewn in).
But having a fixed protagonist seems to be the default in JRPGs or Japanese action RPGs, and I haven't added any of those yet. Apart from Trails in the Sky, there are a couple more that come to my mind mind that might fit the description (Grandia 2, Gurumin, Chantelise, Recettear etc.). Thanks!
EDIT: I added all the JRPGs and Japanese style action RPG-likes / Zelda clones. I haven't checked out yet who the main characters are, so if anyone spots a game with character choices among them, that should be on the other list instead, let me know!