Are you arguing from a theoretical or practical standpoint? In practical cases the FPGA products do solve my first two issues, as the video output path of the emulation goes directly to the display output in the FPGA. Meanwhile in all software-based emulation products, the video output path goes through a normal Linux graphics stack, which tends to be crap (and not getting better with the silly X11 vs. Wayland fight that keeps Linux's graphics stuck in a bad spot).

That's not an inherent limitation of software emulation, no, but for all practical purposes it is as nobody is doing specialized software emulation for a specific set of hardware to bypass the normal OS/graphics stack. It's instead "throw linux on it, and fullscreen an off the shelf emulator"

> FPGA doesn't really solve your other two issues, nor is it practical for anything post-PlayStation/Saturn/N64

I agree with most of your point here, bus is that particular one true? Doesn't the Gamecube (for example) use a PowerPC chip? I would be very surprised if isn't an effort to make FPGA implementations of the PowerPC.

I realize that there's a lot more to making a clone system than "just recreating the CPU", but why would making an FPGA for something after the N64 be impractical?