Well, the difference between the GBA and DS are very great. Its true how someone managed to make an exact copy from Genesis to GBA and it worked, but still. The GBA isn't really built for a perfect collection of Genesis games, and isn't as powerful as the Genesis itself.
The DS however, is like the 64, and is portable. I heard the 64 also struggled with 2D games, but the DS is able to do them just fine.
Seeing as how that is, and how Kingdom Hearts 358/2 Days and Super Mario 64 DS turned out, I'm sure this'll turn out great. Especially since SEGA has done some pretty amazing stuff for us the past year.