Pokemon Sun/Moon
Fire Emblem Fates
SMT IV
Fire Emblem Awakening
Bravely Default

I don't really play RPGs on the 3DS, but from what I have played:
Pokemon Sun/Moon
Fire Emblem Awakening
Fire Emblem Fates: Revelations (although the other two are probably good too)

1. Fire Emblem Awakening is the best by far. The story, mechanics, gameplay, and characters just mesh perfectly. Fates may have more refined gameplay, but the story doesn't jell with the mechanics anywhere near as well.

2. Pokemon (any of them). I feel like Gen 6 and 7 were the best since gen 2.

3. Bravely Second because the first had that repetition issue in the latter half.

Haven't really played the others, but I'd guess Monster Hunter and Dragon Quest 7-8 would round out the list.

1. Fire Emblem Awakening
2. Pokemon Moon
3. Persona Q
4. Fire Emblem Fates
5. Bravely Default

SMT: Devil Survivor 2 Record Breaker - Awesome isometric tactical RPG that combines SMT mechanics with strategy based combat. Features a relationship system similar to the Persona franchise, only without the time management aspect. This is a remake of a DS game, but improves on it with an entirely new 30+ hour story. My favorite SMT game, and also one of my favorite RPGs ever.

Fire Emblem Fates (Conquest) - I'm only picking this one out of the three sub-games, as I cared more about the gameplay, story, and characters in this one than Birthright. Story is a lot simpler than the GBA or console games, but the mechanics have been refined to a point where I find the gameplay here to be the pinnacle of the franchise so far.

Fire Emblem Awakening - Similar reasoning as Fates: Conquest, only the mechanics have a lot more issues. I like the characters in this better than Fates, but I found the mechanics to be lacking in comparison, and the difficulty to be far too low for the the franchise standards, even on higher difficulties. The story starts off really solid, but goes downhill in the final arc, which is why I put this one below Fates, on top of the aforementioned mechanics.

SMT: Devil Survivor Overclocked - Another DS remake, which adds about 10 hours to the original this time. The story in this one plays a lot closer to the mainline SMT franchise, and captures the macabre and dread much better than the sequel. Unlike the sequel though, the characters weren't nearly as interesting in this one, and your relationship between them is largely unimportant, outside of a few characters that grant additional endings.

SMT IV / Apocalypse - I have a tough time ranking between these two, since they somewhat tell the same story. The first game does a much better job at telling a story, and handles plot twists a lot better, but really suffers from a lack of interesting characters. Apocalypse handles the characters a lot better, but really relies on events from the first game to propel the story forward. Overall, both are solid for different reasons.

Pretty much just two franchises, but god dang do I love these franchises. Stella Glow (which I haven't played yet) and Fire Emblem Echoes both have a solid chance of entering this list...though we'll see soon!

1. Shin megami tensei apocalypse
2-5 in no specific order. Bravely default, persona q, fire emblem awakening, dragon quest 7

Hornorable mention. monster hunter generations because im not sure if it counts as a jrpg

1) SMTIV
2) SMTIV: Apocalypse
3) Persona Q
4) Fire Emblem: Awakening
5) Bravely Second

Fire Emblem Fates

Tales of the Abyss

7th Dragon III Code VFD

Pokemon Sun

Shin Megami Tensei IV

3DS games:

1. Pokémon X
2. Monster Hunter 4 Ultimate
3. Dragon Quest 8
4. Fire Emblem Awakening
5. Pokemon Sun

Honorary mention to FE Fates Conquest and Bravely Second

1. Xenoblade Chronicles
2. Dragon Quest VIII
3. Dragon Quest VII
4. Moster Hunter Stories
5. Etrian Odyssey V

(not counting the FE strategy games, Fates and Echoes world be on 4rd and 5th place)
Honorable mentions: Bravely Default, Bravely Second