It's just a pity that Gunnar thinks (or thought) that just creating software patches will get him round any hardware incompatibility.
Well, in a sense this is in good tradition. CBM also had to come up with software patches to make the Os compatible to the 68040, and third party vendors had to add even more software patches to make it compatible with the 68060. That is nothing I would worry about "too much". It had to happen in the past.
I'm more worried about "removing potential" by Gunnar making design choices of what he believes "is useful" and "what is not useful".
Granted, for the majority of Amiga users, the MMU is "not useful" and the FPU is "not useful", but maybe there are a couple of folks out there that believe that these units can be made good use of here and there.
The current design is not the end of the story, of course, and I don't want to demand too much too early, but the general attitude seems to be that there is "no need for this nonsense", and that type of attitude is probably a bit dangerous.
There are other problems I foresee, as redefining the meaning of some of the Motorola opcodes. The current core puts the 68020 opcodes CALLM/RTM to some completely different use. Again, both instructions are worth nothing on the Amiga, have never been used, and cannot be used productively, but for a "clean room" implementation, I would prefer if the team would stick to the list of opcodes Mot defined in the 68K family guide, and simply trap for instructions that are unsupported, even if unsupported for a reason. The 68030 and up did not support these two (again, for good reason), but that does not mean that this particular opcode "is free for everyone's use". Leave it reserved, do not touch it - it only confuses development software such as debuggers or disassemblers that - with this change - can no longer decide what an opcode means without knowing the host CPU.
Thus, it is really the process how this FPGA core is being developped, not so much the core itself. Gunnar is certainly a very knowledgable guy when it comes to CPU designs, I do not doubt this in any way, but it would certainly help if the team would look a little bit more to the left and right and would understand that some other people (not only me) also have a story to tell for a reason.