i'm using the latest stable release 0.5.2. I discovered that the other games just play fine, with some minor sound issues, which are normal for a gba emulation, so I think that Mother 3 is a very difficult game to emulate, but maybe i'm wrong. In particular i have problems when, after selecting all the names, there's the screen with all your choices made. Then I select ok to start the game and there's an incredible slowdown, even if fps counter stays stable, but the game, after all of this, plays fine. For clearness I'm using Mother 3 fan translation 1.1 version.
Well, I just read the document that comes with 1.2 patch and it names all the issues i'm having with Mother 3. So I don't know if I can do anything about it.
I downloaded and applied the italian patch v. 1.1.1 (cause I'm italian, but I didn't know it existed) and.......it worked great! The authors were able to get rid of the issues the english patch has; they showed this in a youtube video, comparing the two versions. So yeah, it was a patch/rom fully related issue. I don't know if I can, but I'm posting the above nominated video:
https://www.youtube.com/watch?v=XP5WDMGFHyk