I own both versions and I greatly prefer the DS version for numerous reasons:
1) Stylus control makes it much easier.
2) There's the ability to make "profiles" for multiple players on the same DS cart. It keeps profiles on gameplay for all three games for the profile.
3) DS version includes Uno Free Fall, which is a Bejeweled-like/Tetris-like game which is a nice time waster for a few minutes.
4) DS version has wireless multiplayer, and multi-player single-cart downloadability.
5) DS version splits the game up onto both screens, with your opponents' cards on the top screen, your cards and the common cards on the bottom screen.
GBA version is $14.99 @ BB, and I picked it up for $9.99 with a GamePro coupon. DS version is $19.99 @ BB, and I picked it up for $14.99 with another GamePro coupon. Problem is, they're both deleted SKU's at BB, so finding them will be a bit on an issue. I've seen both DS & GBA versions at Target, though it's been a while.
Between the two, the DS version wins hands down. I wish I hadn't bought the GBA version first, though I couldn't find the DS version anywhere, and I lucked out at BB on a random stop-in. Either one is nice for a quick portable Uno fix, though get the DS version if you can find it.