I would go for PCI without a doubt :-)
I have a Prometheus with Voodoo3 and it runs quite well. You'll notice that it will be faster on 3D, blitter, etc. The only point where it would be worse will be in bus bandwitch. Another good point is that in the future you'll be able to upgrade your gfx card by a Radeon easily.
Another nice option would be an Algor+Norway module (USB is cool and baing able to do a cold boot and use USB mice and keyboards thanks to the flashrom is great).
But I think that the best option would be a Prometheus :-) You won't have many drivers but you'll be able to put a cheap RTL8029 (some friend may give you one) and you may plug a Voodoo3 PCI or Radeon PCI.
Even if you keep the Permedia2 I would go for the Prometheus.
Mediator 4000T is nice but much more expensive
