@IowaBrewer I know its a bit late but i had these issues with my old pi2 it was the cheap nasty usb cable i was using. I bought a decent one and my power supply's worked well. The same thing happens with the dirt cheap hdmi cables as well sometimes.
@TheGamer What games in particular are you having issues with. The original NES had lots of slow down, and emulators are doing exactly what the original NES did. If the sound doesn't sound choppy, but sounds normal, its just the original slow down in the game.
There must be something wrong in your setup. RetroPie on a raspi3 with decent peripherals can run smoothly any game from the 8/16-bit era without any tweak. Just install, config input, put your ROMs and play.
[Footnote: OK, maybe 3D games, like StarFox (SNES) and Virtua Racing (Mega Drive), can stutter a bit. But the games you mentioned should work just fine.]
I'm a total noob at this. Got the Pi today and followed a guide to install the emus. NES, SNES and Genesis works perfectly. But on SMS there is a small latency like 0.3 seconds or something. It's hard to do precision hits and jumps. Is there a simple setting somewhere that could possibly fix this?!
Second: Turn your TV to gaming mode. Connect the HDMI from the Pi directly to your TV and bypass any soundbar etc. Often this latency is caused by post-processing from a TV, AV receiver, soundbar, or other device that the HDMI signal is passing through.