Well, I got the game a few weeks ago, and actually played it through 100% normal completion in no time; a real testimony to how fun this game is. I was just hooked. The gameplay is simple, yet great and I wouldn't mind another Metroid like this.
Anyway, the plotline; the most controversial aspect of this title...
Loved it.
Sure, Samus' monologues often have a sense of redundancy. Sure, all exposition is thrown at you after the final boss. Sure, the Deleter plot was dropped last minute. But in what this title was actually moving towards, Adam's final sacrifice, the game delivered big time. Even the infamous Ridley scene worked courtesy of the atmosphere, environment, music, and the gradual build up of Little Birdie to Ridley. And I'm willing to ignore the story's other flaws because of that.
Whilst I could have done without the Power Suit suddenly vanishing like that, or otherwise some show of feat in the Zero Suit here and there, I felt the game gave us plenty of justification for Samus' sudden PTSD attack. The most obvious premise having been discussed here before: Ridley and the Space Pirates being completely obliterated in the destruction of Planet Zebes. Adding to that, we shouldn't forget loss of the baby, her fated meeting with Adam, and the doubt cast over all her comrades thanks to the Deleter.
Looking at Samus' normal interaction with Ridley, it's notable that she's always completely isolated, or with only a computer to talk to. This feeling, known as a classic metroid staple, would help bolster Samus' emotional defenses against such a shock as Ridley's inevitable return. But now, meeting the people closest to her, all her emotions being dragged out into the open ready to be broken by mistrust; Samus' cold and harsh bounty hunter exterior can only be maintained in gameplay, not in cutscenes. She even monologues this weakness of her; she does not open up to people for that very reason. A concept I find working exceptionally well in relation to her behavior in all previous Metroid titles.
Of course, none of this can hold up until we accept the first premise; the destruction of the pirates. Which revolves on a whole lot of paradoxes between Prime3 and Other M. The important one here being the Pirate Homeworld; one of the pirate homeworlds. Which would implicate the Space Pirates being a much greater organization than simply the planet Zebes.
But is this really the case? Prime1 describes them as interstellar nomads, and makes clear Zebes was their primary base of operations, if not the only one. Following Tourian's destruction the Space Pirates split into two; Zebes and those that ended up on Tallon IV. The pirates we see in subsequent titles are just an extension of those that left Zebes. Unlike Tallon IV and Aether, this "Pirate Homeworld" would simply be their biggest base of operations since Zebes, from where they are lead by Dark Samus to become Prime3s antagonists.
With the Galactic Federation's attack on the Pirate Homeworld, everything falls back to Zebes, where Mother Brain has been slowly recovering, perhaps with the assistance of Aurora Unit technology stolen from the Federation. All neatly working its way toward Metroid II, Super Metroid and also Other M; we just need to accept that the Aurora Units are nothing compared to Mother Brain herself. What with lacking her telepathy to control Metroids.