I've always had lower end hardware than my peers (still do, except at work!) so maybe you had a different experience than I did... But here goes my experience:
Emulators are much harder to play than the original console because milliseconds matter! Maybe not so much for puzzle games (like the Zelda franchise)[0] but certainly for action titles...
I don't know much about this "RetroPie", but it sounds like a raspberry pi, probably running an emulator on Linux. That's not hardware.
On NES hardware, your controller had a very real, physical connection to logic gates on the CPU (which happened to have a very real, physical connection to the electrons being shot towards your face by your TV!)
When using an old Nintendo, (or SNES, or N64, but only for SOME games) you got to experience your own limitations. The machine was faster than you, it never got hand cramps, etc. But it clearly wasn't smarter, it wasn't BETTER. People had beaten these games... So could you. You just have to try harder! You'd find yourself doing funny little things like holding the controller differently and trying to just shake your button finger, not actually raise and lower it, to fire as fast as possible...
When you finally did beat a game, you beat the exact same game, the same experience that other players faced, down to the millisecond.
...
0: Sure, there is some skill, but quite frequently the goal is to unlock some door or get some item. I never had any trouble playing Zelda games on emulators.