I have designed part of a CPU in an FPGA, and that was pretty cool, and very satisfying. I think it makes a lot more sense to synthesis in this form.
Simulations are really good for prototyping as well, if one is able to provide reasonable modelling parameters. Usually doing something in FPGA, one already has a pretty good model to work from.
I did some FPGA projects in uni, and the design - implementation - simulation - realisation - test cycle works very well. It's beautiful to see it come together.
I haven't done any complete systems on FPGA though. Never had to. If I do any FPGA designs now, I would probably use an existing free or commercial CPU core, with my own peripherals designed around it. I think you have a much more keen interest in computer architecture than I do though. I would be more interested in getting applications programmed and running, rather than focussing on the core.
