I'm going to deal with these separately.
Samus caring for the baby Metroid is from 1994's Super Metroid, a major plot point of the game, which was explaining the ending scene from 1991's Metroid II: Return of Samus on GameBoy. The TV commercials and comics surrounding Super Metroid's release touched on Samus' bond with the baby Metroid.
Wrong. The plot of the game is to rescue the baby metroid which was stolen from the Federation labs. Now her going to rescue it could have some feeling involved about caring for this creature, however, I want to note that the question here is whether she cared about it like it was her
child. The space pirates and Ridley/Mother Brain by extension are assholes as has been shown before. They are going to treat the creature horribly and try to use it somehow to bolster themselves in someway or another. The "feeling" here could be: 1) To stop them after they stole something which could potentially make them stronger 2) To stop them from mistreating the last animal of its species. So the reason for the rescue isn't some I can't live without the baby level thing but to stop what could be developed by an evil organization after studying it, something the Federation would do as well but that's beside the point.
Super Metroid Game Over screen
You have to get back the thing that was stolen from your employer.
Super Metroid intro
(Turning on the Japanese subtitles shows that Samus uses the term "baby Metroid" 3 times. This is also used in the Japanese box and manual.
http://www.metroid-database.com/sm/super-metroid-20th-anniversary5.php)
First off I'm clearly basing myself on the English version here, second this shows the baby metroid's feelings towards Samus not the other way around. She's speaking very matter of factly as to what happened.
Super Metroid manual -
http://metroid.retropixel.net/games/metroid3/manual/
Even this hardened bounty hunter could not destory the Metroid larva. When the larva sensed Samus presence, it clung to her as though it had found its mother.
This doesn't serve as a good way to explain why she did not shoot it. It could imply she felt like she had to be merciful with the newborn instead of having any feeling of motherhood with it. The same as can be argued that she saw the value in preserving the last of the species. This is very vague.
1994 Super Metroid Promotional Video (Japan)
http://youtu.be/quR5-FEaM9c
"The Baby Metroid! I definitely heard it just now! The Baby Metroid is calling for me! I was the first thing it saw when it was born, so the Baby Metroid thinks Im its mother. Im the only one who can get it out of here!"
Again this is a Japan specific thing and not only that it's part of the propaganda for the game. I don't consider this an accurate reflection of what Samus might feel towards it as it shows in the games. Even then most of that is just stating what happened, with the last part being the only one that might show that Samus cares for the metroid, but even that can be argued that she's the only one who can rescue it because she's the only one capable to fight against Ridley, Mother Brain, and the rest of the space pirates. So it's vague.
Nintendo Power Super Metroid comic by Benimaru Itoh - 1994
http://www.metroid-database.com/manga/listing.php?vid=1
August 1994 - Shounen Oh Game Comics Super Metroid Manga
4 panel gag comic referencing Samus as the baby Metroid's mother
First, who even is that guy? Second, it doesn't even make sense. Samus has been surprised and "not sensing danger" many times in other games and none of this has made her get hurt so much as it appears to show here. Another thing that's inconsistent with the rest of the in game universe. Also being distracted by the thoughts of something else doesn't mean that she feels that strongly towards the baby metroid. It's importance could just be that she was distracted in thinking about how to go about rescuing it or some such thing. Again, this is vague but it is also inconsistent. Third, really a gag manga? Are we supposed to pretend that's part of the characterization of the character and not just a joke about it?
http://www.retrogamer.net/retro_games90/the-making-of-super-metroid/
Sakamoto: As the last scene depicted Baby Metroid being born right in front of Samuss eyes
well
theres no real explanation for that in the course of the games, but that scene was another source of incentive for us in that we wanted to follow on from that ending, linking Metroid II with Super Metroid. We were determined to keep the same world-view and maintain the continuity of the story.
http://www.gamasutra.com/view/feature/4333/the_elegance_of_metroid_yoshio_.php
Sakamoto: "I was very moved by the last scene in Metroid II, and that stimulus became my motivation and inspiration in creating Super Metroid.
From Super Metroid on these were mostly handheld games through this period even if the partner changed, I was still working on the project. The central character of Samus, the strong fighting woman who didnt shoot that baby Metroid at the end of Metroid II, was something that I made sure I protected, even as we went through all of these different projects with different partners. - Yoshio Sakamoto
And here we finally have something from Sakamoto himself. Now before I go any further, this is also the man who wrote Other M which has a fundamentally awful, inconsistent, and incoherent story. At the time though, that hadn't been the case yet so you know things might be different but I just want to put that out there first.
The first quote does nothing to show any sort of feeling Samus might have for the baby. He says they want to link the games' continuity and the world view through it. Ok the continuity is fine but world view would be what? It's themes? Metroid 2 isn't really about motherhood and Super Metroid doesn't seem all that much about it either. I can see an argument for the latter but even then to me it's more about professionalism in retrieving a stolen good than any specific feelings for the creature akin to being her own child.
The second quote says how Samus is a strong fighting woman (ironic to see this fromt he same man who wrote Other M's plot) who didn't shoot the baby metroid and he wanted to protect that. Ok that's fair and that's, again, just a statement of what happened. She did not in fact shoot the baby metroid even though her mission was to exterminate them. She is also a strong fighting woman. What we continue not to know is why she did not shoot it when it was born. The same way an argument can be made that she felt motherly feelings to it, for some random reason, the argument that she saw value in preserving and bringing back the last of the species to study in captivity can be made.
Metroid II: Return of Samus (1991)
http://youtu.be/W4RYxluUBVo?t=4m
Samus defeats the Queen Metroid in an intense battle. The music changes to a lighter tune and the baby Metroid that hatches makes happy noises around Samus.
After a tough battle there is a moment of reprieve where "the miracle of life" happens. The light tune could just be there to illustrate the fact that it's not hostile to Samus but also serves to show that it sees her as its mother, but that doesn't mean she feels the same way.
I chose to disregard the Other M gifs because that is exactly what I'm arguing against and as already shown by the difference with the Super Metroid CG scene in this game, this remade scene can also change things to try and justify it's clumsy and senseless "story". Second, even using it you can see that all she does is stand around surprised at the fact that it doesn't attack her which does not indicate a sudden feeling of motherhood in her. Third, in the last set of gifs you're just going against your own damn point. If she felt anything for that first baby metroid why would she shoot this one since it reminds her of it? Adam shot her in the back because he's an asshole he's going to kill them all anyway it's just more confirmation that the story is idiotic. Samus is not "acting" out of her character given that this whole game isn't even based on her actual character to begin with, so this is a non-argument.
We can't infer anything whatsoever and if you're just going to sit here and tell me you were reading Samus's mind when Thing A happened in Super Metroid or Thing B happened in Metroid Prime then I'm afraid you'll be having this conversation with someone else. None of which even begins to broach the whole damn point which is that her behaviour in Other M, at least where Ridley and the Metroid are concerned, makes sense, regardless of whether that's how someone would want Samus portrayed.
What? So you can make that argument but somebody else can't? And did you even see any of the videos they linked? It CLEARLY shows that Samus isn't freaking out when Ridley appears but is either annoyed, frustrated, both, or AT MOST surprised by the fact. Nowhere does she even come remotely close to the same reaction she had in Other M.
And no it really doesn't. She's faced him so many times before without having that reaction, why would she now? How does that make any sense? It doesn't make sense in this game to show her like that especially now of all times. IIRC the game doesn't even bother to mention that he killed her parents, so it just makes it an even bigger question as to why she'd react like that. And even if it did say that, it still doesn't validate it since she's battled him before and was perfectly fine. This reaction makes no sense no matter which way you look at it.