Well ... SC and M3/G6 still have a better compatibility with NDS-Games and that counts at least to me
pretending a game is
incompatible when its problem is as tiny as
"Music stutters when loading next area" is a little bit far-fetched
If you ask me about the DS-Xtreme compatibility, I'll tell you that only 1 game doesn't boot (Animal Crossing) and 1 game doesn't save (Madagascar is the only one afaik - i may be wrong). And a few games have minor glitches like music stuttering when loading, etc.
But the other solutions also have these kinds of issues in some games! Look at the M3 wiki if you don't believe me!
I'd say that at the moment, the M3/G6 and DS-X compatibility are equivalent, as the M3/G6 currently don't support the Tony Hawk game.
What's more, the M3 requires you to be careful when you burn a game.
You sometimes need to try different settings before the game works properly.
Also the M3 doesn't support download play, in every game. The DS-X does support it in almost every game.