I haven't personally tried playing gba games as of yet so I don't have a "I tried it so etc etc" answer. But from what I've heard, fat16 in 64k cluster size will run your gba games fine, only difference is that you may have to use start instead of A to launch the games. But it will work just fine, lakersfan earlier confirmed this and many others are confirming it on m3-forums as well. It's just that you may have a longer loading (a couple more seconds) when starting the gba game with start instead of A. This does not affect the actual gameplay @ all, just startup. And to IZA, the increase in speed is for DS games, on gba games it makes no difference.
Whats the difference between starting with 'start' and 'a'? I know it's "demo" vs. "game", but what is the technical difference?