Every single plot hole in Metroid: Other M

Metroid: Other M. Love it or hate it, it is still riddled with plot holes.

* Why does a species that starts out as a bird thing with 2 legs with backwards bending knees Metamorphose into a quadrupedal lizard, and then again into a bipedal dragon with wings on its back, instead of into a wyvern, with wings on its arms, as it's first form would suggest?
	+ Why would it need two stages of metamorphosis at all?
		- Why would it go months without showing significant growth or changing forms, and then suddenly grow to fifty times its own size in one day?
	+ Why didn't Samus's scanners identify it as Ridley, considering it has encyclopedic knowledge of almost all known life-forms in the galaxy and the ability to make conclusions about what unknown organisms might be based on their physiology?
		- Why didn't Samus, Ridley's mortal enemy, know anything about his species?
	+ Why didn't the scientists who cloned it know anything about it either? Why would they not realize it wouldn't be best to leave the door to an enclosure with a creature with rows of razor-sharp fangs open, and why would a scientist go in there without any form of protection?
	+ Why did Ridley toy with Samuswhen he was fully grown, and not try his best to kill her when he was in his second form?
* If the Space Pirates aren't sapient and can't function without the direct control of Mother Brain, how did they put her back together after Samus blew her up the first time?
	+ How does Mother Brain control Space Pirates presumably committing space piracy out in space, far away from Zeebees and well out of what should be her zone of control?
	+ Why can't she control other non-sapient creatures?
* If Mother Brain was the culmination of years of work by the Chozo, how were the humans able to consolidate the technology to fully replicate her function in a brain 100 times smaller, in two months?
	+ How does MB function without the presumably necessary giant brain to control the various bioweapons on the BOTTLED SHIT?
	+ If Mother Brain rebelled against the Chozo because she was sentient, why would the GF think that copying the functions and personality of Mother Brain into another thing that is sentient wouldn't also cause the exact same result?
		- Why did they not at least install a Kill Switch in her?
		- Why not install a Kill Switch in EVERYTHING?
	+ If MB dies from gunshot wounds, how did she kill the BALEETER, despite not having protection from the bioweapons or anything else?
	+ Why would the GF attempt to physically capture an android that they knew could overpower them according to their specifications?
* Cold always hurt or sedated the metoids because they're energy based organisms, and cold is the absence of kinetic energy. How did the GF "breed" that out?
* Why did Scumbag Adam sacrifice his life to blow up Sector Zero when he knew that at the end of the mission the GF was going to blow up the whole ship afterwards?
* Why did Samus not tell him she saw things that had been killed by metoids and knew that at least some of them were outside Sector Zero?
* Why was the clone of THE BABY able to produce cold resistant metoids despite not being one of the metoids with the genetic modification to do so?
* What were those purple crystal things?
* How did a splinter cell of the GF manage to hide a PLANET SIZED space station, which they presumably stole somehow?
	+ Why would they build a giant 50 acre enclosure of lava to store contain samples of, like, 4 or 5 creatures?
	+ Presumably the place was full of scientists, but when Samus explores, she finds a grand total of one body. Where did the rest of them go? Did they have time to all escape? If they all escaped, why would they send a distress call?
* Near the end of the game, the BOTTLED SHIT starts heading for the GF. Why was this supposed to be a threat? Wouldn't the GF, a massive interstellar government, see the fucking METAL PLANET coming from ten million miles away?
	+ How was it planning on delivering its payload of monsters to a GF planet without crashing into it and wiping out all life anyway?
	+ Near the very end a computer says that the BOTTLED SHIT was "Approaching GF Orbit". The GF is an interstellar government, did they mean it was outside the galaxy's orbit until then? Or did they mean that it was entering orbit with the capital star/planet? Why didn't the GF react sooner if that was the case?
	+ Instead of sacrificing himself to stop the metoids, why didn't Scumbag Adam just stop the engines from his place in the goddamn CONTROL ROOM?
* Why did Scumbag Adam have a highly trained Galatactic Federation Assassin on his crew? Was his crew composed specifically to answer the BOTTLED SHIT's distress signal? If so, why not send 6 specially trained operatives, rather than 5 normal guys and one killer?
* If the BALEETER wasn't sent there to kill Scumbag Adam's men, how did he know he had to kill them at all? He couldn't have received any communication, as it was all being jammed. Why would the BALEETER kill the platoon during the mission rather than afterwards?
* How did Scumbag Adam recognize MB's face if he had never been on the BOTTLED SHIT before? Did he know all this shit and just decide not to tell Samus?
* If it was MB's plan to use the cloned Zeebeesian monsters to get revenge on le GF, why did she wait out in space until the GF sent a team in to actually start doing it?
	+ Once she knew the GF was on board and probably planning to kill her, why didn't she immediately surround herself with those nearly indestructible ball creatures?
* Why would the GF send only six dudes to search for survivors in a space station the size of the Death Star?
* When they discovered it was full of incredibly dangerous bioweapons, why did they continue to investigate with their pea shooters and soccer pads instead of establishing communications with the GF and tell them to send properly equipped troopers to come clear it out, or even just make the reasonable and nearly correct guess that everyone was dead or gone?
* Why didn't Scumbag Adam do anything about the BALEETER?
* If the Splinter Cell wanted to clear evidence of their crimes, why did they send a double agent into a hostage recovery team instead of just self destructing the station or set it flying out into deep space?
* Why?

1. ↑ I think you know.