"Next to nothing is known of his pre-military background (if in fact he even had any), but it is safe to say that he made his way up the ranks until finally he was designated leader of the Space Pirates in battle."
I don't know why it needs to be assumed that Ridley needed to move up in rank. The Space Pirates seem to act feral if there is no one to direct them. Mother Brain mentioned to Samus in the manga that the Space Pirates are like worker bees. Anyway, in Metroid: Other M, there are four times that Little Birdie howls. I can only remember three right now.
- When Samus first encounters the Griptians in the Biosphere, Little Birdie makes a howl. All of the Geemers and Wavers seem to disappear until after Samus defeats the Griptians.
- When Samus is in the room where there is a waterfall, and where Reos and a Dragotix is sleeping, as soon as Samus changes the room by using the terminal, Little Birdie makes a howl.
- When Samus enters the Keyhunter nest and notices Zeros, Little Birdie makes a howl, which causes the Keyhunters to go into a frenzy.
Aside from that, there is another instance where creatures appear as soon as the adolescent form of Ridley howls. Once this form of Ridley leaps onto Samus, he howls, and all of a sudden there are Reos, Griptians, and some other creatures. Furthermore, when Samus is listening to MB, MB tells Samus that some presence caused the creatures on the Bottle Ship to go into a frenzy. Adam Malkovich even makes note of this.
"Despite his fall, he somehow survived, possibly due to an initial Phazon mutation in the impact crater, or possibly due to the strength of his cyborg modifications."
It seems that these two cannot come to an agreement. We don't know how Ridley survived the fall. All we know is that he did. Does this really need to be here?
"It's interesting to note that Ridley's disintegration (unlike other Leviathan guardians) was never actually seen."
Ridley's disintegration is seen. The camera just diverts barely away. I've been told that Samus' ship does not count Ridley's death, however. I don't know where this is shown.
"Even after these devastating battles, though, Ridley manages to rise again, this time with a purely organic body."
Not really. The real thing that occurred here is that after Samus battled Ridley in Metroid, Ridley made another appearance in Super Metroid. That's all this really is. I am not even sure if the Metroid Prime trilogy is actually canon. This works well for a story, though.
"but just before Samus is mortally wounded, Ridley leaves as the space station's self destruct sequence begins."
I wouldn't say Samus is "mortally" wounded.
"With the loss of the armor plating from his previous form, [Ridley] is now much more vulnerable to attack. His previous form demanded that he be shot in the chest or mouth, but he is now vulnerable to both Missile launchers and Charge Beams from any angle."
The real reason is because the side-scrollers did not, and have not yet required the player to fire Ridley's mouth or chest.
"The fact that Ridley is fully organic in this game is a call for theories from many fans of the games."
I have a theory. It's called retconning. Before Super Metroid, there wasn't a Prime trilogy.
"His color changes from Brown and Black (as in Zero Mission) to Purple after corruption; according to the chronology, this is most likely a choice by the designers, but can be explained that the regrowth of his organic parts bleached him purple (he does appear Purple in the Smash Bros. games and the original Metroid). Another, much simpler theory is that the Pirate group that stayed on Zebes cloned him from DNA taken before or after his initial defeat on Zebes. As to why he returns without any cybernetic enhancements is possibly due to his previous defeats in the Prime series which may have left him wary of robotic abilities."
I don't understand this. The most likely choice is by the designers? Of course! Just as much as the appearance is chosen by the designers. There really is no need to add unnecessary things that we know for certain aren't true. If I saw that the sidewalk was wet, and I saw that the asphalt was not, but the grass was, would I say, "It must have rained"? Of course not! The most likely thing that happened was that someone used his or her sprinklers to water his or her grass.
Metroid: Other M
"[Ridley] still has an organic form similar to his appearance in Super Metroid, indicating that he may still distrust cybernetic enhancements."
No. The most likely answer, and Samus thinks so, too, is that Ridley was cloned. This has nothing to do with Ridley having trust issues with cybernetics.