Yes, you're correct.
For Genesis, Master System and Game Gear use Genesis Plus GX
For now, the only core for SNES available in the repo is Snes9x2010. I've seen that CATSFC works better, but I need people's feedback on this. If it works great, I'll add it as a module.
As for the N64, I've seen that GLupeN64b works better than Mupen64Plus
Classic Controller should work, but I don't have one, so can't say for sure
I need more details on what did you do, PM me, please
Thanks again for the reply. One last question: how can I check how much free space I have on Nes mini? Because I keep adding and adding games