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Idk, the end of that fight was vague as heck compared to the other Seed Guardians, who we explicitly saw disintegrate. Ridley just started sinking into the ground while glowing, then Samus and the camera look away as a bunch of Phazon gets expelled into the air and he has disappeared by the time they look back. Given that we know that he did not die (among other things supposedly the counter keeping track of the number of killed enemies does not go up like with other bosses), the implication seems to be he just vented the excess energy the same way Samus periodically did in both cutscenes and gameplay and then... hid underground? Flew away? Idk, lol.
When we first see him in Prime, he is covered almost completely head to toe in metal, and the logbook even notes that the only real weak spot is his chest where the armor is lighter-but-still present.
When we last see him in that game, he is exploding at the bottom of the Impact Crater, and two seconds before that he is getting lasered in the chest by the Chozo security system.
All of this is consistent with his Omega form, where large chunks of his armor have been lost, there are more (and larger) exposed organic bits, and his chest has an obvious gaping wound in it that the logbook even points out for the people who miss the camera zooming in on it.
The problem is that that is *not* consistent with the fight at the beginning of the game, where Ridley looks like this. Apart from being waaaaay bigger (more liek Roid-ley amirite), he seems to have more armor and fewer biological bits than even his original incarnation in Prime, there is no wound to his chest, and in fact his torso now has enough metal-plating that it is no longer even a weakpoint in-game anymore.
Given that Samus only does damage to his mouth and that the fight simply ends with him falling down a hole that he apparently pretty-quickly just climbs out of, there is really no logical reason for his Omega form to look the way it does after that. All of the traits that we could attribute to being battle damage from the showdown at the Artifact Temple just sort of reappear without any apparent cause.
"I think I also noticed a plothole in AM2R, since the Gravity Suit can resist lava"
Lower Norfair's lava in Super and Magmoor Cavern's lava in Prime also damage the Gravity Suit. Evidently it has limitations. ¯\_(ツ)_/¯
"maybe that's why it was changed to acid in Samus Returns"
That and they wanted to change it to a liquid that the Chozo put in there to contain the Metroids so that they could have those DNA statues that Samus uses to lower the level instead of the more arbitrary 'Five dead Metroids triggers an earthquake' progression of the original.
"In regards to Metroid Prime 4, the existence of Metroids still puts it before this game"
Right, I was talking specifically about how at the moment Ridley's design goes through a logical progression from the end of Corruption - Samus Returns - Super Metroid where he has progressively fewer cybernetic enhancements with each appearance.
Depending on what they do with him in Prime 4, they could in principle screw that up.
"Other M make even less sense on why they have a Queen, (disregarding the fact that if you can clone these things why have the need to keep a Queen.)"
In fairness, they did not *need* a Metroid Queen in Other M, nor were the GF planning on it. They were just randomly cloning all the gunk off Samus's suit willy-nilly without knowing what any of it was. That is why they accidentally cloned Ridley (and I guess Phantoon, somehow, despite being a ghost (~_~) ). The Metroid DNA they used just happened to be for a Queen.
Although that just raises further questions, lol. Samus did not actually run into any Metroid Queens in the course of Super. The only Metroids she came into contact with were the Infant and its copies, and if the Infant is supposed to just be a baby Metroid Queen, then why is it that all of the other clones of it (which share the same DNA) are normal Metroids? The ones in Fusion (who are also clones of it) all go through the standard life cycle. The whole point of recreating their native planet was sort of predicated on that. >.>
"I think I also have an idea on why Metroid cycles fit solely on Samus Returns and Fusion"
Iirc, Fusion says that the Metroid life cycle works that way in those games because that is how Metroids evolve in SR388-style environmental conditions. Apparently, that is also why the ones bred on Tallon IV are comparatively weak and able to be killed with just standard power beams shots if shot enough.