VLB performance should not be underestimated. After all it was a much simpler bus and it had direct access to 486 memory bus.
Rather than performance which should be similar, I would consider whether you will be taking advantage of:
- PCI IRQ sharing - allows to install more expansion cards
- larger selection of PCI expansion cards which are newer and have more memory. You could use a 3D graphics card in 486.
- the board will likely come with AWARD BIOS which supports larger drives than those old non-LBA AMI BIOSes
- PCI PnP (not a big advantage in my opinion)
I would also vouch for PS/2 mouse connector due to ability to use optical mouse.
If you would benefit from the above advantages then I would pick PCI board even if it had slightly worse performance than VLB board.
Pentium III 900E,ECS P6BXT-A+,384MB,GeForce FX 5600, Voodoo 2,Yamaha SM718
Athlon 64 3400+,Gigabyte GA-K8NE,2GB,GeForce GTX 275,Audigy 2 ZS
Phenom II X4 955,Gigabyte GA-MA770-UD3,8GB,GeForce GTX 780
Vishera FX-8370,Asus 990FX,32GB,GeForce GTX 980 Ti