Hmm.
I never mentioned 3D, I was thinking in terms of cost effectiveness as 3D isn't an option if you opt for zorro-II anyway.
So, looking only at 2D:
The biggest problem with PCI systems available is that the CPU<->PCI bandwidth is typically quite lousy (not that much faster than accessing Chip RAM under AGA). This is the limiting factor for video and 3D, which generate a lot of traffic. That said, the CPU<->Zorro-II card bandwidth is actually *slower* than accessing Chip RAM under AGA.
A typical voodoo3000 card has a far faster blitter and pixel clock than any Z2/Z3 graphics card currently available, making it a lot better for 2D (of course, you need to make sure you are not using little endian modes).
You have a point regarding the native screens however. One solution is to fit a tv card and route the native video through that.
I'm not knocking Z2 cards, I've used one in the past, but you have to be realistic. Performance wise, they offer little compared to the PCI solutions currently available. Your contrary experience seems to be the exception rather than the rule.