The original Pong is still good in the context it was meant for (a bar or arcade), if you run into one somehow.
Since you mentioned the NES specifically: Super Mario Brothers 3 holds up the best, but they still make Mario games that are just as good, so I think Mega Man 2 would be my biggest recommendation. In either case, I'd consider an infinite lives Game Genie code; standards changed for the better there.
You're right that early 3D looks terrible. Except Doom, which still rules.
I think older games generally become less playable over time, but the high points tend to stay around a long time. The old games people say are still great aren't nostalgia, they're survivorship bias. Using SNES RPGs as examples, everyone says you should play Final Fantasy 6, Chrono Trigger, Earthbound, maybe the other Final Fantasies and Lufia II. But nobody recommends Breath Of Fire anymore, even though at the time it was considered good enough to have a whole series spawn off of it.