PCI on a 486 was an eye to the future, but some stability and/or compatibility problems existed with software made for the 386 era. It was also the first iteration of PnP.

VLB on a 486 was basically souping up the 386/486 architecture and thus was quite stable for games expecting that hardware. Dealing with hex addresses, IRQ's and non-PnP hardware may be a headache initially, but was more stable than the 486-PCI combo. PnP didn't get practical until the PII era IMO.