Although Amithlon certainly looked promising and had advantages, I agree that UAE can pretty much do the job anyway now. And it's free, most importantly free as in speech, so we don't need to worry about petty squabbles killing the development.
Surely a migration to x86, whether it's just a port or updating the OS, would only be possible with a port of AmigaOS, otherwise you're just running an emulation of 3.9?
I'm not sure what speed differences there were, but considering the how far CPUs have come since 2001, it's not really a significant issue - WinUAE on any PC now will be way faster, and ridiculously faster than any real 680x0 Amiga.
Note that WinUAE allows Amiga programs to run native x86 code too.
