Initially it seems odd that Ridley went to SR388 to get Metroids all by his lonesome. If the Pirates wanted to capture as many Metroids as possible, a whole hunting party would be a better choice. But the Space Pirates don't need several Metroids; all they need is a single Metroid larva so that they can multiply it with beta rays. And given that Ridley is strong enough to tear a Metroid larva from his face, there's no sense in wasting a significant portion of Pirate forces just to capture a single specimen (especially when a Metroid breakout at Old Tourian killed all of the Pirates there).
Also concerning the fight with Ridley, it also justifiesRidley being vulnerable to the Power Beam in Super Metroid's prologue. He's only recently recovered from both regenerating what parts he still had implants for, and had only just picked himself back up from getting his ass kicked in this game. Sorta makes sense he wouldn't be at 100% when he raided Ceres, and why the Power Beam affects him when it never has before, assuming one disregards the original Metroid as Early Installment Weirdness.
There's their All There in the Manual name Proteus Ridley. "Proteus" was a shape shifting Greek sea god whose name is the origin of "protein"; "mutable", "capable of assuming many forms", or in modern use, organic matter. If you assume "Meta" from Meta Ridley is meant to refer to Metal or Mecha, "Proteus" can be inferred as Proto. Any or all of those would fit Ridley, who's in the midst of transforming from his cybernetic to his original organic form.
As noted under the Nightmare Fuel entry of Samus Returns, the Zeta Metroid resembles a lot more the Xenomorph from the Alien franchise. If you dig a bit, that actually makes some sense. The Metroid in general has a lot of inspiration and homages to the Alien franchise. Heck, the Zeta Metroid's first appearance in the game closely resembles the Xenomorph's debut in the first Alien movie, making the homage all the clearer.
Diggernaut being able to One-Hit Kill Samus during the Advancing Wall of Doom segment seems like the usual situation where a boss is much stronger before you actually fight it. However, in this case, it actually makes sense in-game. When Samus fights Diggernaut with the Gravity Suit and multiple Energy Tanks, its drill arms still inflict 150 damage. By contrast, Samus only has the Varia Suit and fewer Energy Tanks during the chase segment, meaning it's entirely feasible for Diggernaut to One-Hit Kill her there.
There have been some criticisms that this game doesn't have the best enemy variety, with many enemies being recolors of older enemies with new tactics or buffed defense. While this may be underwhelming from a gameplay standpoint, it actually makes perfect sense within the story. The manga explains that the Metroids killed 80% of the wildlife on SR388. Anything that could survive in the same ecosystem as a population of Metroids must be incredibly tenacious and aggressive, and enemies display these traits very well ingame with their tendency to rush you headlong and the high amount of damage they deal.
Area 7 is the only part of the game with ice and frost covering the ruins. This is also the laboratory where the Chozo bioengineered the Metroid species. They either intentionally chose the coldest part of SR388 in order to keep the Metroids docile and under control, or the laboratories are kept refrigerated by machinery. Since this shows the Chozo knew about the Metroids' weakness from day one, they may have intentionally designed the Metroids with a weakness to cold in order to be able to contain them.
During the final boss battle, absolutely none of its attacks are counterable until the Metroid Hatchling starts draining him. It's possible that this is because, until that happens, the final boss has been keeping its guard up during its assaults to avoid getting countered by Samus. Unlike the Metroid bosses, which lack the sentience to understand that some of their attacks are counterable (and thus will repeat them), the final boss is intelligent and knows full well what Samus is capable of. The reason that the counterable attack happens after the draining is because it's not JUST draining his life energy, it's also temporarily hindering his ability to think clearly. This is what makes him perform a reckless and suicidal attack immediately afterward in a fit of rage, leaving him wide open for a counter attack from Samus.
In Metroid Fusion, the larval Metroids view Samus as their kin and therefore do not attack her, but an Omega Metroid still attacks Samus on sight and tries to kill her. Why do the different stages of Metroids behave differently? A subtle answer can be found hidden in the Chozo Memories of Samus Returns. When the Chozo created the Metroids, they were able to successfully control the larvae and live peacefully with them. However, when the larval Metroids metamorphosed into Alpha Metroids, they suddenly became much more aggressive and Turned Against Their Masters. Therefore, the heightened danger and aggression of the post-larval Metroid stages is the reason why an Omega Metroid is the Final Boss of Fusion.
There are fan complaints about how Samus Returns increases enemy density in the later areas in the name of combat, whereas the original reduced their density to emphasize isolation and horror. The depiction in Samus Returns is also viable for atmosphere, but not for the same reasons: up until Area 5, there are signs of various lifeforms that aren't innately hostile to Samus' presence in the background to go with the hostile indigens, but they become less and less frequent until they disappear altogether. It's more an issue of natural selection than anything; the only lifeforms that tend to exist in the presence of an apex predator are either invasive species or creatures that have best adapted to the predator's presence. This means that every creature within range of an Omega Metroid, let alone the Queen, is either capable of nonlethally fending off an Omega through sheer numbers... or another Metroid. Also, bear in mind: what are the Metroids going to eat if there's nothing there? Rather than some ubermonster that mindlessly consumes everything in sight, the remake depicts the Metroids as an apex predator the planet's lifeforms adapted around, despite the Metroids being artificial in origin.
The fact that there's a non-evolved Metroid to be found on the Surface before any of the purple liquid has been drained seems strange at first, but it serves as great foreshadowing of the fact that the Metroids have already found a way to the surface that bypasses the Chozo's methods of containing them. The first Metroid fought in the game didn't come from Area 2 and below, but directly from Area 8 through the back entrance to the Queen Metroid's lair, which is only blocked by crystals that are specifically vulnerable to Metroid attacks.
As discussed in this "mini-review" of Samus Returns, the controversial melee counter mechanic actually serves a greater storytelling purpose. It brings direct attention to the fact that the wildlife of SR388 is hyper aggressive, likely due to having to survive in an ecosystem where Metroids are the apex predators. In particular, each Metroid (except the Larva Metroids, which still make a beeline for Samus and attack her as soon as they see her) performs an attack that can be countered, enforcing this idea that the counter mechanic demonstrates the violent hostility of SR388 fauna. Furthermore, this forces Samus to be cautious, often times waiting for enemies to attack before countering. How is this significant? It further highlights the disparity between mature Metroids and the baby Metroid, which is the only Metroid (and now, in this remake, one of the only SR388 inhabitants) that does not immediately attack Samus on sight. Samus charges up her Ice Beam and waits... but the baby Metroid does not attack. After everything Samus has been through during this mission, the complete lack of hostility from this baby Metroid stands out to her as significant and unexpected, which is why she decides to spare its life.
Bag of Spilling and later retcons aside, why can't Samus use the Scan Pulse, Lightning Armor, Beam Burst, and Phase Drift in the later chronological games (Super Metroid, Metroid: Other M, and Metroid Fusion)? Because these abilities require Aeion energy, and her suit has a limited gauge that can only be refilled while she is on SR388. Her Aeion supply is most likely depleted by the time she visits the Ceres Station, Zebes, and BOTTLE SHIP. While the BSL Station does replicate the SR388 ecosystem (and possibly, with it, Aeion energy), Samus's Fusion Suit has lost all her old abilities, leaving her unable to use any Aeion energy if she found it.
The Diggernaut makes use of a suction attack against you, which you have to exploit to defeat it. As shown over on YMMV, the Diggernaut encounters are rather divisive, with some calling it That One Boss. The Diggernaut sucks. Well played, Mercury Steam.
Why isn't "the baby's" egg with all the others in the Queen's room? Because it's a Queen itself! Metroid: Other M explicitly states that the DNA to clone a queen came from "the baby".
As awesome as the Metroid hatchling fighting against Ridley is, it really shows why Metroids are The Dreaded. Ridley's durability to the point of No One Could Survive That! being the norm, and Samus, a One-Woman Army, is the only being who's ever been able to best him, and he's still the one thing she's ever been afraid of. A newborn Metroid is able to pull The Worf Effect on him! Imagine what the stronger Metroids are capable of. Or remember the implied Curb-Stomp Battle Ridley receives from the Queen Metroid (which was cloned from the baby Metroid) in Other M. How would anyone else fare against them? That's what the Space Pirates would weaponize if Samus didn't repeatedly stop them. There's a good reason the Galactic Federation declared it necessary to wipe them out (publicly).
The baby Metroid removes crystalline barriers in Samus' path on the way out of SR388 to get back to her ship. You've seen these barriers throughout the entire game blocking paths and expansion tanks from you but the hatchling works through them like they're nothing. Which makes the barrier go from annoying to terrifying when you realize the only way that it makes sense is that they're crystallized X parasites. And you've been touching and Spider Balling on them almost the entire game.