Final Fantasy IV
Holy grinding, Batman! I stopped playing this as soon as that summoner girl joined the party at freak'n level 1!
Chrono Trigger
I think I got stuck in one of the worlds and couldn't figure out where to go. >.>;;
Majora's Mask (N64)
I just didn't like this game. The 3-day cycle was annoying, and I just generally dislike games which include a "race against time". The plot and storyline also did nothing for me, so though I was at about 85% completion with the game, I stopped playing.
Final Fantasy VIII
This just got so repetitive and boring, and after a particular event on the third disk which just annoyed me (along with the "badguy who never dies"...aka, that one enemy you have to fight 3-4 times in the game before he/she/it actually DIES), I never finished it.
Final Fantasy XII
I hated the new combat system, the characters felt flat and bland, and I just couldn't get into the story. Oh, and I kept getting lost in the first town. Yea...that one didn't last very long.
Disgaea
Got bored of it in the first dungeon. >.>;; I really loved Final Fantasy Tactics and how it worked, but this was just...dull for some reason.
Yu-Gi-OH GX Duel Academy
I really loved solving the puzzles (practicing them and on the "exams"), but the rest was too easy or too boring/slow. It was annoying to try and trigger events, too. So, never finished it.
Pokemon White 2
This was...possibly the worst Pokemon game I've ever played, and that's including Gen I games (crappy sprites, mass amounts of glitches, etc). I stopped after the second or third gym, I believe. Heck, I don't even know why I still own this game.
Hometown Story
I've played some bad games, but I've never played a game as bad as this. And when I say "bad", I mean it was terrible and should never have been made. If I hadn't purchased it through the eShop (and on sale to boot), I'd demand my money back.
Bravely Default
Chapter 5+, man. Chapter 5. I might eventually finish it for the cutscenes, but I know how it's gonna end, and what it'll take to get the true ending; I'm not thrilled with the work which needs to be put into it to get there (aka, the grinding. Thank goodness I'm abili-linked with one person who has mastered every single job class, at least).
Fantasy Life
I should really finish this...I think I left off at that port town.
Rune Factory 4
The only reason I haven't finished this is because I got distracted by other games. I already cleared what's probably half of the game, but I still have some to go. I do plan on coming back to this one.
Borderlands 2
I really should finish this. I forgot where I left off. >.>
...I'm sure I'm forgetting some, but those are the ones I recall off the top of my head.