Chrono Cross, but not the entire time.
I don't know if that really counts.
Serge and Lynx swap bodies, but it's not like Lynx went Magus and had a change of heart, or Serge-Lynx suddenly decides to be evil. Now, in the sense that Serge not dying sort of fucked everything up that Crono and co. did... Yes.
Mary in Persona. Arguably.
Same as above, kind of, although it's ALSO arguable whether or not Bad Mary is really that much of a villain.
Xenogears, sort of.
Fei and Id were the same person although I'm not really sure Id was much of a villain and I always thought that was a really stupid plot point. Then there's the other thing where Elly is Miang and Fei, Lacan, and Fei's dad are all the same person only not, and Ramsus is a clone of... one of their progenitors, who was also Fei.
In like Fallout you can be a villain if you want. Like, go around planting dynamite on children and then watching as they scamper into a church or something. The game even notes this. Elder Scrolls games let you do this to although to a much lesser extent. and technically you can be evil in the Ultima games but this is sort of counter intuitive to *winning*.
In Wizardry IV you play as the villain from Wizardry I.
Wizardry IV is pretty much the most impossible RPG ever. Also I'm not sure it's even canon. Also Werdna's not really that well developed.
I don't want a hero or a villain, honestly. I want a Jake Barnes. Like...http://www.storybites.com/babelgoose2.htm
A meek person capable of doing terrible things and wonderful things and sort of opting to do both.
But maybe for that to matter you need more choice than JRPGs really provide.