Ocarina of Time: Yes, I know it wasn't released this year, but I finally got around to actually playing it like 3 months ago. I can see why it's a classic, and it does hold up - even if the "legendary annoyance" of the Water temple was toned down for newbies like me. (I never really got into classic Zelda - it was way too cryptic for me.) The entry into the Zelda universe is pretty good, because it still feels epic without turning into cryptic city.
Heroes of Ruin: It's a pretty decent game, if you handicap your character on purpose. It's fun and creates an atmosphere of community (which is rare in a 3DS game). I loved picking your character and working in tandem with others. (Although, there are too many stupid Gunslingers around.) I can't wait to play this again with my Epishock vibrational speaker in my dorms - it will be great!
RE: Revelations: Playing through the first hour of this was pretty awesome. I generally hate the RE franchise, but this game still feels like survival horror. (It's freaking poop your pants scary, sometimes.) It also not brain meltingly stupid storywise, and still feels plausible (yes, suspend your disbelief for a moment).
Rollercoaster Tycoon 3D: Yes, I know some of you are saying...NO! (Because it's a cut-down version of the original, but still - it's awesome.) That may be the nostalgia talking, although.
As for the others you've mentioned:
Tales of the Abyss: The graphics and other stuff is amazing, but I'm totally not a fan of this fighting style in RPGs. I can see why it gets good, and I really should give it a chance. (I loved Tales of Phantasia on the GBA.)
VLR: Sounds interesting, and that reminds me, I should finish 999. Problem is, I'm not that into visual novels, and solving weird logic bombs that the dev's have put into it.
Kid Icarus: I've been scarred by Zero Punctation's review of this game, what with particle effects and the NOT BEING ABLE TO move your 3DS when you play it. Seriously, I have my 3DS because it's portable, and seriously awesome.
Kingdom Hearts: For some reason, I never got into this series. It could be because of the terribly cliche storylines, and the good vs evil motif. (You know it's terrible when an anime freak like me says it's cliche.) I feel like I should like it or have better reasons for disliking it so much, but hey, an opinion's an opinion! I love the idea of the weapons - the keyblades in particular.