Well, having everything on a sigle fpga allows every possible hack, pseudo unlimited in chip connections, implementation of a SoC network (like dspin)...
For example dspin can handle something like 10GB/s traffics without problem. To have such traffics on pcb would probably require more work than just a simple include.
As said before you could also devellop the mcu or cpu instruction set, modify cache access methods... Of course this requires (a lot of) work.
There is also the advantage of beeing able to run coprocessors on the same chip. This could appear to be simply a (possibly huge) performance gain but it is also the best way to work in continous time (not on clock edges).

I currently work on a system based on mips R3000 which is a "free", parametrable mips, that can of course be ported to fpga.
If you are interested about this project take a peek on :

http://www-asim.lip6.fr/recherche/disydent/

Basically the suite allows to devellop embedded systems in very short time, using the same code for host simultion, target system simulation and hardware synthesis

I know this is not fully 805* related but I m sure you won't bad karma me :-)

Best regards,
Benjamin