I spent a few months trying to get Linux running on a commercial CPU core on an FPGA. This was in 2004 so I don’t know how things have changed.
My FPGA(Spartan3) could only run the CPU core at 50MHz. Not exactly WOW…
FPGAs are expensive compared to a CPU chip. If you want speed that you need Xilinx Vertex or something like that, which runs into the $100s of dollars, only comes in BGA and you need $$$ for the synthesis tools.
I used the Microblaze CPU from Xilinx, which made like A LOT easier than taking some VHDL source and adapting in to your needs. Microblaze had a nice GUI to configure the core and to select all the peripherals you needed. Even with this things where really daunting.
I would say, if you need SMP then use a dual core CPU. If you need reconfiguration then use a standard CPU and add an FPGA.