I'm here to explain suggestion in more details.
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What new features you desperately want from WinUAE?
1. MMU emulation (as it was required by A/UX and Linux distributions)
2. Full SCSI/IDE emulation (Softmac has it, also SCSI support was in build 142)
3. Since WinUAE can emulate full range of 68k processors, new Basilisk should be expected to emulate all 68k models from 128k (maybe even Twiggy prototype) to 68040-based Quadras and Powerbooks (and with QEMU PPC core plugin range would be extended up to PowerPC G4, so new emulator would be successor of both Basilisk II and Sheepshaver)
4. Emulation of expansion cards (NuBus graphic cards, Apple IIe card, DOS cards/addons, etc.)
So, maybe it's not about porting new WinUAE engine to current Basilisk II, but about making new emulator with old name.
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For example, JIT was broken. But in my experience there is no need to be fixed given the fact that nowadays CPU is fast enought. I haven't experienced sluggishness in the old Mac game I got. I'm happy to live without JIT.
You can turn off JIT in WinUAE, so it would be optional here. Also, the JIT compiler in WinUAE can only be used with 68020 or higher emulated CPUs, and is not compatible with MMU emulation.