Zero Mission ruined things that made Metroid excellent. It's just not obvious on the first playthrough. Unlike previous Metroid games, you can't really do Zero Mission out of order. There's a path you have to follow and if you go elsewhere the road is blocked by Chozo statues, that weren't present in the original game.
While I agree it's a core element of Metroid, and I completely understand how it would bother many fans, but for me this is one of the less-essential aspects of Metroid. But it's possible that much of my initial enjoyment was because I had played Metroid Fusion before that, which is much worse as a Metroid (while still fun as a game).
It could also be because I got 'hooked' on Metroid because of Metroid Prime, and IIRC that one also was a bit more linear by virtue of the hint system.
Yes, Metroid III (SNES) was the last game in the series that let you go off track. I've played through it many times and never took the exact same route. Everytime it's a new experience. It's unfortunate that the games that came later copied pretty much everything from Metroid III except for this.
