And while I know nobody cares about them, here's my opinions anyways.
Golden Sun shouldn't have been on that list. The original games are overrated as hell and Dark Dawn wasn't much better.
Bowser's Inside Story is way too low, especially in light of the many VNs that got rated over it (admittedly, I'm not the biggest fan of VNs given the whole "I don't find the writing amazing enough to offset the complete and total lack of gameplay."). This should've been at least within top the 15.
Tales of Hearts, lolwut? Call me when it actually makes it outside of Japan.
VNs. Half of these should have never made the list and should make room for actual games. That said, I'd say keep Hotel Dusk, 999, Ghost Trick. Maybe not where they are but keep them on the list.
Chrono Trigger is debatable. Obviously it should be lower just by virtue of only having portability as the only meaningful change made to this particular port. The rest of the changes are the usual Squeenix cramming in that ROM Hack Supra Dungeon +1 and littering it with Swords of Infinity +1. No bonus points for the useless monster arena and terribly shoe-horned in extra ending that exists solely to do a hilariously bad job tying this game into Chrono Cross.
FFIV I'd rank lower, but not by much. The fact that it's an actual remake (although maybe not the best remake, I would still rank it a better job than either FFIII or either of the FE games got) does justify it's presence on the list, but top ten is a bit much.
Radiant Historia should've made top 3 easily, shoddy production values be dammed. It's one of the biggest game changers in JRPGs in the last decade, losing out to an Ace Attorney game is unacceptable.
DQV and Devil Survivor. I can't say anything on Devil Survivor as I haven't played it yet but I do suspect that it this weren't SMTFan it wouldn't have made top 10 let alone top 3. DQV is a port of a remake, but admittedly its also the first time it's left Japan and its a damn shame that it took so long, I have no beef with it's placement.
And TWEWY. Yeah, objectively this is probably the correct decision, but only because it has better production values than RH got.
And for notable absences. FF:4HoL, maybe Infinite Space, and either Knights in the Nightmare or Rondo of Swords or VP: Covenant of the Plume or DQVI or FE:New Mystery of the Emblem (although debatable it did receive a fanslation) or LoZ:Spirit Tracks or Pokemon Black/White. One or two of the above (man, there were a lot of mediocre and/or stranded in Japan RPGs for the DS; there's like another half a dozen games that could've made the list if they had just left Japan (yes, including ToH)).
Ninja Edit: I will say thank you for not including more than SMT:SJ for dungeon crawlers. Those fuckers were everywhere and most were mediocre as hell.