I apologize.
I didn't realize that I was using the 0.4.0 over and over again.
Previously, I downloaded the latest build from just clicking on "Wii" at the Download section, I didn't realize that there was ANOTHER download just below for the nightlies.
Dumb me haha.
Anyway, I already tried the latest one, here are my results for the Wii build:
1) Gameboy games boot now, (Gameboy COolor games do too!)
The only weird thing is that when I boot one GB/GBC game the lower portion of the screen appears all glitchy, the part below the actual gameplay size. I am using Stretched mode for the record. There's a little fuzzy sound for GB/GBC games too, but I think you're already aware of it.
2) I don't know if its a bug or not, I chaged the default input method to Classic Controller and switched A and B to Y and B, saved the config in both inside the Input menu and in the main menu too, but when I switch games, the configuration seems to default.
3) I am getting a boxed output instead of full screen with Streched in the menu.
Out of that I think that's pretty much it.
I'm amazed that the Gameboy Color games actually booted, I wasn't expecting that.
The only suggestion I'd give is to add a way to detect GBC mode for GB games so that they show up in color.
Hope I'm not bothering you too much about this feedback, endrift.
I just want to be of help.