The problem with trying to use the FPGA to do more than just the control functions is that you would need to hook it up to more places on the Amiga..
Need it to simulate an IndiECS (Assuming you had a powerful enough FPGA, which would probably shoot the price WAY up), you need to hook it up to the Denise chip as well.
Need it to do AGA?
You need to hook it up to ..er.. um.. everywhere.. the whole board.. :-)
The reason it can do the RAM and IDE is that those can pull right off of the CPU.