One of the main differences between these two great games are:

1. In DS, you play as a boy, and in DS Cute, you play as a girl.

2. In DS, you play as the standard boy from the SNES, FoMT and more games, but in DS Cute, you can play as Jill, or Clair OR Claire? I'm not sure which names the right one. Jill is the brown-headed girl with two ponytails from AWL Girl version, even though I don't play the game, I just know!  And Clair/e is the blonde one from More Friends of Mineral Town!

3. DS: 4 special girls DS Cute: 1 special boy

4. DS has a few glitches that can be used to your desire, while DS Cute is de-bugged.

I'll add more later!