It really depends on what you want your hack to do.
GBA roms are great in the sense that the state of ROM hacking is really advanced, meaning you have a lot of freedom to do lots of really neat stuff.
DS roms are great in the sense that they already have a lot more stuff in them (physical/special split, pokemon, etc). Although you could put them in by hand if you're so inclined, it's kind of a pain.
So I guess if you have a really ambitious hack that changes maps and entire gameplay mechanics, GBA roms are best. If you want to do a purely story/scripting/tuning hack, DS is really going to be the way to go.