I love Conception II! It's actually my favourite JRPG on 3DS lol. But like you, I also wonder why I love it so much haha.

1. Conception II
2. Fire Emblem Awakening
3. Fire Emblem Fates
4. Persona Q
5. Project X Zone (This one introduced me to tactical RPGs, which lead me to Fire Emblem :D)

Pokemon Y was fun. Moon too, but the lack of global pokedex really killed the drive to "Catch em all".
Rune Factory 4 was another great one.

I have yet to play Shin Megami Tensei Apocalypse, its still on the shelf. I'm also interested in Stella Glow

Persona Q, as a game, is a lot closer to Etrian Odyssey rather than actual Persona. I'd serve high praise for its music, graphics, and adaptation of the Persona system into a (generally) flexible Etrian Odyssey sort of dungeon crawler. I recommend it to anyone who wants to get into Etrian Odyssey, but if you want to get it as a Persona game (which, quite frankly, most people are going to view it as), it's rather poor.

My list:

1. Stella Glow

2. Shin Megami Tensei: Devil Survivor 2 Record Breaker

3. Etrian Odyssey IV

4. Persona Q

5. Etrian Odyssey Untold

I have to say that I bought the 3DS to play a Fire Emblem game, and Awakening (while a fun SRPG) is pretty bad at being a Fire Emblem game. Conquest has some of the best SRPG mechanics I've seen yet, but it has garbage for a story (though the supports are quite nice).

I'm also trying to finish 7th Dragon III, and it's also a great game from the third that I've played so far. That said, it's a bit too easy; I once got into a fight with seven Dragons at once, and beat them all without a party member dying in the midst of battle. I do think I am overleveled, though, I kill every Dragon I come across!

I think I haven't played a single one xD

Edit: Ok I remember played Mario & luigi: Dream Team which was ok, but that's it

1. Persona Q
2. Pokemon Omega Ruby
3. Etrian Odyssey Untold
4. Fire Emblem Awakening
5. Etrian Odyssey IV

Very debatable. ;-o

My top:

1. Fire Emblem Awakening

2. Project X Zone

3. Bravely Default

4. Code of Princess

I've played some others, but I don't like any of them enough to be considered good enough for any "Top" list.