The story was made by Sakamoto, not Team Ninja.
He needs an editor then.
More like 3,000 editors. I seriously have no idea how come it crossed his mind it was perfectly OK for this game to have:
1) Samus saying "this was the first joint mission I'd been a part of since becoming a free lance bounty hunter", implying Prime 3 and by extension, Prime 2 and 1 didn't happen or are not canon, or were moved to happen much further ahead into the Metroid timeline, which would then contradict the expected lasting events from Fusion's ending. This pissed off a lot of people within the very first 20 minutes into the game. This could have been easily fixed/prevented by having Samus say "this was the first joint mission I'd been a part of since the Phaaze crisis" instead.
2) The Hell Race. Samus never even questioned Adam why it took him so long to "authorize" her to turn on heat shields when that's not even a weapon to begin with, or why he didn't tell her or recommended for Samus to activate her shields before entering the Pyrosphere as per his own orders. This means she was willingly OK with following orders to her death by that point in the game, which is disgusting. The context of this situation could have been easily fixed/prevented by simply having the following dialog before entering the Pyrosphere:
Adam: Samus, the Pyrosphere is a really dangerous area with a high heat signature. Be sure to turn on your heat shields before entering the area. No other weapons are authorized until further notice.
Samus: Roger that, Adam.
Or, as an alternative to keep the tension of having to speed-run that section:
Adam: Samus, be careful. I'm detecting a strong interference that's affecting your suit. You won't be able to turn on your shields for now. Proceed with extreme caution as we can't risk failing this mission by attempting a rescue in the Pyrosphere. I'll try to resolve the interference but try to cross the Pyrosphere as fast as you can in order to minimize damage to your body.
Samus: Roger that, Adam.
But instead we silently got by virtue of context:
Samus: Hey Adam, I'm dying here because it's extremely hot. Can I at least turn on my heat protection? It's not a weapon.
Adam: No.
Samus: OK, I'll just keep dying here until you feel like it. I'm a good girl trying to impress you, so I won't disobey you right now.
There's absolutely no defending that.
3) The Botteship's security mechanism. You seriously tell me the engineers of the Bottleship made it so it requires for someone to die in order to save the ship in case of a Sector Zero leak? What if they send a person that dies before reaching the switch? "Um... Any other volunteer?"
4) No one seems to fear Samus Aran here. By this point in the Timeline and considering Prime, she has destroyed several planets and even raided the Pirate Homeworld by herself. Her fame would precede her by her merits and accomplishments, and no sane puny human army or soldier (Including "The Deleter) would dare to even piss her off, yet the federation tries to arrest her at the end of the game like they actually can, which is hilarious to even think a bunch of puny humans would be able to scratch the paint job of her armor. Yet she is still working with the Federation at the beginning of Fusion. Samus can't be that stupid.
5) The PSTD scene. Won't even start with what's wrong with it. People will cite the manga to reference why it's canon when the Manga has Adam dying.