I believe the OP was not talking about using a development board, but a custom designed one to fit in a miggy. The price of a Cyclone 2 chip alone is not that much (definitely cheaper than a second hand 68060 these days).
The only drawback here is that Cyclone 2 is a 3.3v chip, and it may require some work to interface it to the Amiga bus. I wonder if the DE2 Tobias used is 5v tolerant ?
Voltage level shifters wouldn't be a big problem to get 5V working.
Put an FPGA with a DIMM slot, mayeb an IDE or SCSI connetor, and you're ready to go. There's something I'd like to do that would be an FPGA on an accelerator card anyway, it would be interesting to allow it to do what I want as well as to act as a standalone TG68 or Natami CPU accelerator as well. Don't think that would add much more to things. Just a couple connectors and some peripheral IPs from OpenCores inside the FPGA. I liek the idea of fitting TG68 into their Wishbone bus, maybe the Coldfire/68K to Wishbone bridge would already allow that. Then it's plug and play with many of the other things there, just need OS drivers. And a different connector for what I'd like to do beyond this. I'd just add a particular connector and have everythign arranged so as not to interfere, a PCI connector treating the entire Amiga computer as a PCI device.