Mmhm, mmhm, all good suggestion, but have you considered a GBA game, as well?
The Golden Sun games are absolutely top-notch, combining the intricate and well-told story of a JRPG and some puzzle-solving skills in the dungeons. Only problem with that is you'll probably want to find a list of the Djinn locations, they're pretty important if you want to seriously pwn the bosses early on.
After that, there's FFVI, of course. IMO, it's the best game in the Final Fantasy series, with a cast of all totally likable characters, unlike the later games, where most people are going to have some problem with at least one of the characters.
Metroid Fusion is like all the other 2D Metroid games, but something that sets it apart from the rest of the series - the Prime trilogy, most of all - is that there of shades of survival horror, and the feeling that you're up against some monsters that can and will mercilessly tear you apart. Unlike the other games where you can go through on your first time with the feeling that you're a real authentic bounty hunting badass, you're going through Fusion with the vague dread of going through a room and ZOMGIT'SEVILYOU!!
Buuuuuuut if you really want a DS game, I'd definitely recommend one of the Mario & Luigi RPG games. They're both great fun, and playing as Bowser in the most recent one is such a breath of fresh air, it's worth it just to play as everyone's favorite antagonist.