I wouldn't use a M3 or supercard in the GBA, I'd get a flashcart made just for the GBA. Thats unless your thinking of upgrading to a DS at a later date. The M3 is meant to be a lot more compatable with GBA games than the supercard. The supercard suffers from slow downs in some games and a few games don't work.
You don't have to buy the M3 lite for the DS but the normal M3 will stick out loads. I'm don't know if the M3 lite fits perfectly into the DS but I know the supercard lite does. If you get the lite for the DS lite you won't be able to use the card in a normal GBA.