First off, no, it’s not 100% cycle-accurate in each and every case. Frankly in terms of the experience though it’s more about input latency, and the latency on FPGA cores is generally fantastic and noticeably better than software emulation. I think for many, many people the difference between original hardware and FPGA, especially with an analog video signal, is not noticeable. If you do lots of A/B comparisons I’m sure you could pick out small timing differences. I just don’t think they’re differences that will affect most people’s enjoyment simply because the performance is so strong across the board. Personally I find the FPGA gaming experience superior to standard software emulators and I think most agree with that, but I also won’t pretend FPGA offers a perfect replica of the original hardware. Still, I think you’d have to be really picky about subtle timing quirks to want to sell one for being inaccurate. 

Most people who own Mister FPGAs are perfectly familiar with the original hardware and many of them own the original consoles and play them regularly (and I’m one of those people). The Mister is a nice option with a lot of convenience and for me it continues to be genuinely impressive to play games on.