So I was thinking of how Other M could be improved upon, short of just gutting the entire plot. I've got a few thoughts, so please feel free to set them ablaze.
[spoiler=Yeah, spoiler tags in case people still give a damn]
-Sector Zero as a playable area. They took a bit of time to build up the area to players and get them excited only to ultimately cockblock them. Samus should have been allowed to go into the area and encounter these so-called Invincible Metroids. Upon finding out that the computer MB that "Madeline" told her about was a hoax, Samus needs to escape the area or else she's caught in the explosion of the colony. At this point, the Invincible Metroids are swarming like mad, maybe throw in an Alpha or Beta stage version as a midboss at any time in this area before or during the escape.
-I'm not sure how Adam's death would occur, but it'd have to be in a way that keeps the GF clear, otherwise, Samus' involvement with them in Fusion would make less sense. Probably killed by "The Deleter" taking a bullet for Samus?
-Introduce the real Madeline Bergman earlier. It's clear with the whole explanation that she treated MB like a daughter that they wanted to build some emotional sympathy with the player. However, as it stands, this is a worthless thing to do three minutes before she's ultimately killed. There's no emotional attachment and it means absolutely nothing other than "that [sonic slicer] got [tornado fang]'d up." This would also work well if MB was actually fought, as now you have the added factor of Samus hesitating to finish her off (she already feels sympathetic to her after hearing Madeline's account.)
One other little thing I and probably others would have appreciated is missiles and super missiles in third person mode while keeping the side remote style. After examining the controller, I found missiles could have easily been set to B, which can be fired with the left middle finger. To use a super missile, you follow a mechanic similar to Metroid Prime where you charge up your beam. You tap B to fire a missile and, bam, super missile.
[/spoiler]