First that comes to my mind is Wild Arms XF. I seem to be the only reviewer who really liked it. Every other reviewer trashed it. Players/fans liked it though, so I'm in agreement with them. And while some weeaboos will always fall into the camp of Japanese voice acting being 100% superior and English voice acting being 100% inferior, I thought the English voice actress for Clarissa was superior.
Now that I'm replaying it, Legend of Dragoon is another one where I like it a lot and most people didn't like it. I especially think the music is underrated. I'll say it: Legend of Dragoon is a good game with great music.
Speaking of music, I loved FFX-2's soundtrack as well. And though everyone loved Breath of Fire IV's music but were meh on Breath of Fire III's music, I preferred III's music. Probably because it was funky jazz fusiony stuff; not the kind of stuff you normally hear in JRPGs (maybe that's why I dig X-2's and LoD's music as well.) I thought BOFIV's soundtrack was kinda generic.
In looking at the soundtracks to FF7, 8, and 9 (the Playstation FFs) most people hail FF7 as having the best soundtrack of the three and 8 has the worst/most monotonous. To be honest, I thought 8's soundtrack was the best of the three. Most consistent, and its tunes just stuck with me.
Oh, and in FF7's soundtrack, Birth of a God > One Winged Angel. Bizarro Sepiroth was also cooler looking than Safer Sephiroth.
On the other hand, Final Fantasy 6 is one game I simply could not get into. I acknowledge that it's a great game. I especially love the music (except the normal battle theme). However, the chemistry just wasn't there. It's like dating a really great girl but that intangible "spark" just isn't there. Like I have to keep justifying and rationalizing its good points objectively and I hate having to do that. Legend of Dragoon could well be considered an inferior game to FF6 (and justifiably so depending on what your criteria are), but somehow I had chemistry with it. That spark. That "za za zu" to quote Carrie Bradshaw from Sex in the City.
And chalk me up as a +1 for enjoying SaGa Frontier. I rented that game just to see how bad it was (since I have a morbid fascination with bad gaming) and I played it for 3 hours straight until a friend called me to come hang out. All I could think was, "This game is really good. Why do people think it's garbage?" Emilia's and Red's paths were my favorite.