Because Snake has multiple faces for expressions instead of using textures like Peach or vertex morphing
like Ganondorf & Captain Falcon, Bonnie has multiple copies of his head and thus has a large file size.

So large that I had to shrink some textures in Project M 3.6's FitSnakeMotionEtc.pac file.
If you're using a custom Snake moveset and Bonnie crashes for you, try replacing the textures
with the included ones and that should fix it.

If it doesn't, then it might just be too big of a MotionEtc.pac file and can't be used with Bonnie.

He's already really low poly, so if I tried to make his file size smaller by making him even lower poly,
the quality would hurt quite a bit.
You can try shrinking Bonnie's textures but be warned that he'll start to look pretty bad.