chip for chip, the voodoo3 is faster than the permedia2, but the system has more hoops to jump through to get to it.
in a nutshell:-
for the mediator
CPU-Zorro3-Mediator-PCI-GFXchip.
for the b/cvisionPPC
CPU-PCI-GFXchip.
when it comes to amiga comparisons, it seems that from what people are saying, it seems to be much of a muchness as to what is faster in both 2D and 3D operations. one might be better at one thing, the other might be better at somethingelse. plus the voodoo has the other added advantage of double the ram for screens and textures.
personal preference, i'd favour the b/cvision as i feel it has a more developed 2D and 3D driver set, and not so "kludged" together... but thats just me.
as you have both, (not that i'm jealous AT ALL) how about downloading P96speed and see what you get? :-D