I'm surprised no one's bothered doing more work on Goomba Color to improve compatibility.
IIRC, Dwedit forked Goomba to Goomba Color specifically to support the GBC Zelda games. He's done a good deal of work beyond that, but there's just inherently a limit to the emulation of the GBC based on the relatively hardware (the number of layers, IIRC)--a lot of games only have decent performance because they were apparently never designed to require running at GBC's speed. Ie, there really isn't a lot of room for improvement*.
Guess there's not as much demand considering GBA can play GB/GBC games natively (even though GB Micro and DS can't, but the latter has Lameboy and Gameyob).
Basically, this. You need something closer to a DS to adequately emulate all GBC games (probably a lot more to do it accurately, but that's another discussion). Honestly, I commend Dwedit for putting as much work into Goomba Color as he has.
* On other systems with higher specs, a lot of emulators start off doing most everything in software and then shift stuff over to hardware to improve performance. PocketNES was only really possible by mapping a lot of functions to hardware from the start. The rest of the forks of PocketNES (Goomba, SMSAdvance, etc) all follow the same trend, so generally there isn't a lot of room to eek out performance unless you start doing tricks like using VRAM as regular RAM.
PS - Loopy, FluBBa, and Dwedit could possibly correct me on some of this, perhaps? I know Nintendo did a (mostly?) software NES Emulator for GBA, but my understanding is it was quite limited in a variety of ways that being software meant it really could be expanded upon. HVCA was some software, some hardware? I think that's the explanation for having better font rendering. This all is of course a generalization.