A little thread bump (since I've played some more RPGs).
The Sword of Hope II (VC) - At 15-20 hours, it's probably one of the most bang for your buck GB games you can download at the moment. It's story and gameplay are simple, but it's a charming DL for RPG fans (and it's neat seeing them try to be cinematic with a GB game).
The Denpa Men: They Came by Wave (eShop) - easily the most time consuming eShop game available for purchase (20-30 hours to beat story. 40-50 hours if you want to do post story stuff). The Denpa Men add a unique charm (and quirkyness) not found anywhere else, but don't be fooled by it's cuteness, at it's core it's a pretty by the numbers dungeon crawler that can get deceptively difficult (especially the post story dungeons).
Crimson Shroud (eShop) - harkening back to the origins of the RPG genre (no leveling in favor of looting for gear, and lots of dice rolling), this game is sure to bring about nostalgia in you old types, yet feel completely new & fresh to us youngsters (like me). It's not a very long quest (averaging 8-10 hours per playthrough), but it weaves one of the more interesting tales you'll find on 3DS, and you're likely to play through it a second time (to get the good ending).
Paper Mario: Sticker Star - Like Crimson Shroud, Anonymous Notes (DSiWare), and many other before them, PM:SS is an RPG that favors item looting in favor of leveling (make what you will of the one time use twist), and it'll take around 20 hours to beat (30 if you aim for all 8 achievements). It's story is more subdued than past entries, but because of the extra attention to detail (everything looks like papercraft), this game is still full of that classic PM charm (I'm a huge fan of the N64 game, and I'm glad to have played Sticker Star).
Tales of the Abyss - It may be a PS2 port, but it's still the most bang for your buck RPG I've played on 3DS (50 hours to beat, 70 including sidequests). The characters are interesting, and the story has some cool twists along the way. It also has a combat system accessible enough to RPG newcomers, with enough depth to keep RPG veterans entertained as well.
Kingdom Hearts: Dream Drop Distance - Probably my favorite RPG on the system (but I am a huge KH fan). The story is pretty interesting to us KH fans, some of the later boss battles are probably the most epic on 3DS, IMO, the production values are top notch, the new monster collecting aspect brings new life (and strategy) to the series, flowmotion is fun to play around with, and you're likely to get 20-40 hours out of it.
This list isn't in any particular order, but just my thoughts on what I've played.