MUGEN doesn't have its source code available, so a direct port wouldn't be possible. There are opensource MUGEN clones, though, so that might be as close as we get to having MUGEN on the 3DS.
You know what? That just reminds me that there isn't really a proper Beats of Rage port available for 3DS aside from that quick port someone made a while back. Seeing as to how OpenBOR is available on practically every other platform, I think the 3DS homebrew scene could use a port too.
1, Mario/Zelda maker
2, Wii U exploit hosting application (can this be done?)
Mari0 is open source, so it wouldn't be that hard.
ARM9 HAX FOR 11.0 PLZ!a 3ds web browser with functioning downloads would be awesome.
Maybe create a homebrew app for 3dsthem.es! Maybe have some really nice UI to download themes and such! Would love to see that!
Another thing you could make is a game like Photo Dojo! People have been wanting a sequel. Maybe for a test you could make it so you draw.
If you don't know what it is it's a game where you take pictures of someone in poses, then do some sounds and then they get used for a fighting game!
Go google it if you don't know what i mean.