Are you seeing a rainbow coloured square in the top-right corner of the screen when the slowdown occurs? If so then you are having power supply issues – your Pi is not getting enough power to it when it needs it which is causing the slowdown.

As it happens, Alien 3 on the SNES is one of the specific games I use to test a power supply on the Pi! It seems to be demanding for some reason, so I know exactly what you are seeing at your end and I would imagine a power supply replacement will sort you out (and you won’t need to change it to CATSFC to work around it).

You need a genuine 2amp (minimum) power supply to prevent such power supply issues. I use a power supply called made by ‘North Pada’ and they are great. Also The Pi Hut 2amp supplies are great too and both can be bought off Amazon.