Patents prevent others form parenting it, even if prior art exists someone can still get a patent and the legal battle to revoke it can be costly if you don’t have large corporate backing.
So getting patents and offering them under an open FRAND license is a good option, some of the most common standards we have work this way.
Ofc if the only reason you get patents is to commercialize them later it’s going to be quite hard to get people to adopt your stuff.
Reminds me a bit of Transmeta. "Code morphing" sounds very much like the instruction reordering that's standard now.
Doing an emulator/JIT at this level has some severe problems & a very sketchy security story. It's unlikely that anyone else wants to do this, and "AOT" solutions like Rosetta 2 are almost certainly the better approach to ISA flexibility.
My bread and butter work isn't very close to the metal, but you sound more experienced with this sort of thing. Are you familiar with the mill? Do you think they have a chance of avoiding the weeds that Transmeta got stuck in?
Maybe all of that is solvable in some way, sure. CPUs can communicate with the kernel through various mechanisms of course, you can build it such that the JIT is a different task somehow that's observable & preemptable, etc... But it's complicated & messy. And very complex for what a CPU microcode typically is tasked with dealing with, for a benefit that seems quite questionable. It's not like there's any reason a CPU doing the JIT is going to be more optimal than the kernel/userspace doing the JIT - it's trivial (and common) to expose performance counters from the CPU, after all.
That doesn't mean a CPU designed for a JIT is inherently bad, it just means doing this at the microcode level like Transmeta was doing is a bad idea.