Not sure if this topic should be Staked, to be honest.
Hmm... Zero Mission, huh? Well, here are my $0.02:
1. Retconned Metroid 1 so that it matches up with the events of NES Metroid as well as Super Metroid, and has references to Metroid Prime as well.
By which I mean, they found a way to incorporate the "Justin Bailey" idea of Samus without her suit running around Planet Zebes. They gave a reason for that to exist and gave you a way to play as Samus out of her suit in a way that made sense.
In addition, they found a way to match up the events of Metroid 1 with the events of Super Metroid. In Super Metroid, which launched in 1993, Samus obviously returns to Planet Zebes. The landscape of Planet Zebes, however, is quite different from what she remembers in NES Metroid, which includes a strange locale on the surface of the planet, in Crateria, called "The Wrecked Ship". Back in 1993 there was no real connection between the Wrecked Ship and anything else prior. It was just an area that Samus had to traverse. However, once you play Zero Mission, you understand why the Wrecked Ship is there, and why it is wrecked in the first place.
The Wrecked Ship is actually a Space Pirate frigate that has been positioned nearby. Upon destroying the BioMechanical Computer, Mother Brain, destroying Tourian (in Super Metroid, this area exists and is basically 'Old Tourian' and part of Crateria), and making your escape, you very quickly find out that the Space Pirates are in low planetary orbit and the frigate has been positioned nearby. Unable to out-maneuver them, Samus's ship gets his, and falls back into the planet, crashes in the area which in Super Metroid would become the Crateria Lake that leads to Maridia. This area is arid in Zero Mission, but has become a lake in Super Metroid. It's possible that the massive explosion that MechaRidley causes at the end of ZeroMission opens up the underside of the Frigate into the Underground Aquifers of Planet Zebes, thus flooding the area nearby. It is also possible that the massive explosion is what causes the massive cloud cover that forces Crateria to, in Super Metroid, be constantly battered by Acid Rainstorms.
You also see that the Space Pirates aren't just situated in Planet Zebes, waiting for Samus to wipe them out. Instead, we learn that the Space Pirates are a nomadic civilization that can easily maneuver through space on its large frigates. This idea seems to match up with what the Space Pirates can do in Metroid Prime, where they take over Frigate Orpheon. Certain image screens in the Space Pirate Frigate Orpheon show the frigate's shape. This shape, shown in Metroid Prime 1, show that it has a similar, if not identical shape to the frigate Orpheon from those image screens. They may be the same type of mothership.
2. Rearranged parts of Metroid 1's map so that the areas started to make some extra sense.
In the NES version, possibly due to memory constraints, rooms in Metroid have lots of similarities. Having helped hack the game in the past, I know that certain room configurations are shared, whether between areas, or between area clusters. In the NES game, they end up just being 'dead end' passages. It's nice that in Zero Mission, they gave these extra passages more meaning, by either housing a cache of items, or giving the player a reason to traverse them. For example, the room where Samus has to hook on top of a device on ceiling rails and traverse acid. In the NES version this area could easily just be skipped, as it would house nothing too important and actually served to slow Samus down. In Zero Mission, it's a necessary part of Samus's trip down and through Kraid's Lair to reach him.
It also did cool things like link the side of Norfair to part of Crateria. Of course, after Zebes's surface destruction in the blast zone of the frigate, none of that would matter (hence why there isn't such a connection in Super Metroid; though there is a connection between Lower Norfair and Upper Norfair that shares a few spiritual similarities).
3. (arguable) Improved and expanded the music of the original game.
In the NES version, Norfair's music is... off-tune, and forgettable. In Zero Mission, it was improved such that it was a bit more lava-like and a bit more melodic. It also added more religious-sounding music to the Chozo Chambers and the Chozo Guide statues, which ties up to the Metroid Prime versions of the Chozo. You know, the Hippie Chozos of Tallon IV.
Man, I kinda wanna go play Metroid Prime now. :3