I've tried adding in RunAhead, and it works okay for some games, but other games crash. FCEUX doesn't really have the "rock-solid savestates" required for RunAhead to work consistently.
Akumajou Densetsu (Japanese Castlevania 3) does this:

This is not just caused by RunAhead. You can also reproduce this in stock FCEUX by repeating this sequence: Save State, Advance Frame, Load State, Advance Frame, then keep repeating. You'll see the exact same glitch happen after it finally boots up.
If anyone wants a testing build, let me know. You can help report bugs.
Another essential feature for reducing latency is Exclusive Fullscreen mode. Without it, Windows adds 3 frames of lag for desktop composition. Seriously, what the hell Windows. FCEUX is still using DirectDraw, and I need to find out if DirectDraw's fullscreen mode works the same way or not.
Meanwhile, I'd suggest contributing features to Mesen instead of FCEUX, as soon as the issue of who owns the new main repository gets sorted out. And I think the FCEUX maintainers agree as well, just look at
thier Github page: "But you might like mesen more:
https://github.com/SourMesen/Mesen"
Here come the fortune cookies! Here come the fortune cookies! They're wearing paper hats!