Multi card set ups are for sure real improvements that PCI-E has over AGP.  As for all of the other things that are supposed to be better, in real world testing of single card solutions with the same card in both AGP and PCI-E flavors, and the same hardware set up, the differences in frames per second are negligable.  Which tells you that the AGP bus itself is not a bottleneck.  It certainly doesn't mean AGP is better, but there's really nothing wrong with it.  The only problem now is that you can't use AGP cards with current cpu's and ram.  If such motherboards were available, and the latest gfx cards were available in AGP, those systems would be just as fast as (single card) PCI-E set ups.

It's just like multicore CPU's: if the software isn't programmed to use multiple threads it just won't be any faster wheter you use single core or quad core.
Same thing is true for multi GPU setups: if games aren't optimised for multiple GPU's, the game will perform the same whether you use a single 4870 or a 4870 X2 or even 4870 X2 CF (for example)
 
In the case of GTL or any ISI based game (rFactor, GTR2, ...) you won't get any benefit because the engine isn't optimised to do so, even of you'd use SLI 3x or quad CF.

Setups with 3 or 4 GPU's can make a difference in some games, but bottom line is that it's just way too expensive for the benefit you get even in the games that can take advantage from such setups.

@Peter Enqvist: I didn't say that AGP is far worse, but it would be wrong to state that AGP is technically better. AGP wasn't the bottleneck when PCI Express replaced it as the standard connector for graphics card and even for today's low and mid range cards it would suffice, I'm not really sure about the (very) high end cards like the HD4870 (X2) or the GTX260/280 though.
Anyway, there is no demand for such cards with AGP interface as such cards would be too expensive to put into an old system and a typical system that still has an AGP slot has too little CPU power to fully benefit from such cards too...