Fire Emblem Awakening is my favorite 3DS game, and basically my favorite game from the last 5 years I'd highly recommend it.
Beyond that on the 3DS I can only personally recommend Mario & Luigi Dream Team (if you like the Mario & Luigi RPGs it's a blast) and Shin Megami Tensei IV as ones I've played that are worth the time/money.
On the DS I would recommend Fire Emblem: Shadow Dragon, FF Tactics A2, DQ IV, V, VI, IX (although IX is kinda a detour for the series so you may not like it). I actually enjoyed FF XII Revenant Wings but it's not the deepest game, Both Mario & Luigi RPGs on the DS are great fun. Unless you are a big fan of the Pokemon Series I actually wouldn't recommend the DS era Pokemons once you've played X/Y, going back will hurt especially without nostalgia glasses (although if you have fond memories of Gen 2 the HeartGold/SoulSilver remakes were amazing fun).
Systems Currently Playing: WiiU, PS3, 3DS
Also Have: Atari 2600, NES, SNES, PS1, N64, PS2, Wii, GB, GBC, GBA, DSLite, DSi, Android (RazorMax), iPhone (4), iPad (2)
