There's are a few things I can think of that need to be fixed respecting Nestopia core emulation issues:
2. Ninja Gaiden - During the intro animation-story graphic color glitch of the moon in the lower left portion. Also reported...
I think I reported that issue a good while ago and soomeone replied that wasn't a bug.
As for the future of Nestopia, I was hoping R.Belmont would take the project under his wing in Marty's absence.