3D is very nice but great 2D art, especially considering the DS's shitty texture filtering, can be great as well but I agree, 3D/2D combination is the best of both worlds, a la Elite Beat Agents.
Not to go too far off on a tangent, but I don't think the DS can do texture filtering at all, can it? I believe developers can perhaps do some anti-aliasing, but it doesn't look like most folks put that kind of effort into DS games.
Phantom Hourglass is probably the paragon of good 3-D on the DS. But I think cel-shading seems to work particularly well with 3-D on the DS, and games like
Double Trouble and
Joker seem to support that notion.
Honestly though, I thought the gameplay and music were really tight in
Children of Mana, but I just have a hard time going back to that GBA look. So many folks say that graphics don't matter...well, for me they do. I won't go into a whole diatribe about graphics over gameplay, but I want the whole kit & kabootle. However,
Ring of Fates actually has some more interesting gameplay aspects, I think, especially later on in the game. Plus, with four characters to control, there's definitely strategy that needs to be considered. It's a double-edged sword, though, because your AI characters are what they are, and they ain't perfect. They fall off edges, fall into water, don't attack often enough, etc. But it's still a really fun game, all the same.