I'm also a Supercard Lite fan. I went with Supercard over M3 because even though I read the Supercard does not do so well with GBA, I am a comitted EFA-Linker fan when it comes to GBA flashcarts. I have a 256mbit and 512mbit EFA, and they kick butt over anything that's DS-oriented on the market now if you're only playing GBA.
As it turned out though, the SCLite does a pretty decent job with GBA. I've heard some games have serious slowdowns (i.e. Yoshi's Island) but I haven't tried any yet that do this. I already beat Yoshi's Island on GBA and SNES, so no need to do it again. The GBA saving procedure in SC is more complex and tedious than on the EFA, but its also more versatile. In fact, there are some GBA games I've chosen to play using the SC instead of the EFA because of the instant-save capability.
AFAIK, the M3 does GBA almost as well as the ol' EFA.
When it comes to running NDS apps, whether it be releases of commercial games or homebrew, the SCLite kicks butt. Saves are done directly to the microSD card, meaning no battery is involved or necessary. The speed is apparently excellent as I see no problems in any DS games I care to play. Patching the NDS games with the SC software is dead-simple. The software client and the firmware's interface are both quite plain and utilitarian, but perfectly functional and QUICK.
AFAIK, the M3 does NDS almost as well as the SCLite.
So, if its for the best all-rounder, and you really want to be able to play anything DS or GBA, get the M3.
If your primarily interested in DS only, get the SCLite. Heck, if you know you ONLY want to play NDS games, get the SCLite Rumble and save a lot of bucks (it cannot do GBA at all, but NDS compatibility is the same, plus it has the gimmicky rumble feature).