While by far not perfect, depending on the game, the Pi can handle the N64, something the MiSTer can't.
Any thoughts on Lakka? I just got a Pi 4 earlier this week and loaded Lakka onto it. Trying to decide which way to go before I get too far into adding games.
Lakka is pretty much bare-bones Retroarch, try it out on any PC or even a phone beforehand, see how you like it. I personally despise the UI it has, no matter the menu driver you use, bloated af and nothing is where you expect it to be, it really requires some time to get used to. Also in my experience some emulators tend to run somewhat worse on Retroarch.