Actually there aren't that many differences between the versions.
As far as I know in LoZ only the soundtrack is a bit different (the Famicom version has slightly better music). And in AoL there are some minor differences, here I prefer the NES version. Someone made a video about the differences:
They're both pretty glitchy, to be honest, and said glitches are game breaking...I like both equally – despite the obvious differences between the two versions, they're still telling the same story and have the same exhilarating gameplay as always
Huh, where are there game-breaking glitches in the first two Zelda games, I never ran into one. I know that in aLttP there's that glitch with the mirror where you can go "under" a dungeon and do several other things, but you must really try to get that on purpose. But in the NES games?
It's mostly problems with cartridges, I can't remember if there are any input specific glitches you can do within the game. I know at one point when I repeatedly entered and exited I think it was Level 1, the game froze on me. I was running a perfectly good cartridge at the time, so I dunno. There are palette glitches and things of that sort, though they're common to all NES era games.
The Famicom versions of the games were a little higher quality, so ideally I'd prefer to play those versions.
The main problem is that those versions didn't make it into English, so I would be playing a game I can't understand. So in theory, I would find the Famicom version superior. But in reality, I generally stick with the NES versions because of the mere fact that they're more readily available in English.