@little
No one is creating new hardware by extending the Minimig cores. And backward compatibility is being maintained with previous real-hardware Amigas by both the Natami team and MikeJ on his FPGAArcade board. It sounds like you may be a bit unclear as to what an FPGA really accomplishes. The A500 core on a Minimig is simply a complete A500 recreated in software and loaded onto the FPGA chip. New "virtual" hardware can be created as needed just by modifying the existing core and loading it onto the FPGA. Therefore everyone who owns and uses a Minimig can load the core-system of their choosing, whether it's an Atari, C64, A500, A500 AGA, etc....
And no one is concerned about x86 Aros running 68K Aros programs because x86 AROS was never intended to have binary compatibility with 68K AROS. x86 AROS uses a variant of UAE to run classic Amiga software and it works just as well, maybe even better than WinUAE since it's integrated almost seamlessly into Wanderer/Zune (the AROS GUI shell). The AROS devs ARE shooting for 68K AROS and classic-Amiga compatibility, which is well underway with the Kickstart replacement bounty.
And if you find that there's an application that doesn't behave well on one of the modified AGA/SuperAGA Minimig cores, then just revert back to a stock A500 softcore on your Minimig....problem solved.
As for programmers/developers being discouraged and not writing new applications for the FPGA Amigas and their proposed "extensions", well, it may be news to some, but that already happened about 10 years ago. Viable commercial software development for the Amiga is dead. Same can be said for next generation "real" Amiga hardware such as the X1000 and the Natami and Minimig. The Amiga is and will remain a system for hobbyists. No one is gonna get rich these days on ANYTHING Amiga, least of all programming for it. But at least with a Minimig, Natami, or FGAArcade people can buy something to relive better times and still have the option to write software for a system that'll be around a lot longer than classic A1200s, A500s, etc. Most classic Amiga users will admit that their systems are running on their last legs, held together with Scotch tape and a prayer.