If you don't mind could you provide a summary of that link?
The best I could do is Sakamoto is George Lucas, Other M is like a low quality Mexican soap opera and the game isn't about Samus but rather all about Adam who is supposed to be awesome but comes across as a douchebag. Samus is just there. Seriously, that link tackles a ton of stuff wrong with the game. I recommend you just save the link in a tab and read some of it over the course of a few days.
Now I've used the cop out of the Federation withholding things in fusion because you aren't authorized for long enough. It's just that a cop out.
Not really a cop out, it's an important part of the story. They don't want to give Samus all her powerups at once because they want to control what she does on the ship. They didn't intend on her getting certain powerups, they didn't intend on her finding the Metroid lab. They purposefully gave her the bare minimum. This was pretty much "You know what you need to know and nothing more".
What defines a Metroidvania? From my understanding (and again please define what it means to you) a Metroidvania has collectables and power-ups.
A metroidvania has an open map to explore with areas just out of reach until you get the required powerup to get there. It focuses on exploration and freedom so the player can be encouraged to backtrack to old areas to overcome things they could not before. There are many secrets spread throughout that you can uncover with the items and abilities you unlock as you progress. Sometimes the game even allows for sequence breaking where you can use shortcuts to get to areas early without having acquired the intended items or passed through certain areas.
It is far more than collectables and powerups, loads of linear level based games have things like that really.
Other M did have both that while lackluster did follow suite with the other games. Missles and the likes.
It's pretty much all it had really, tank upgrades. On the rare occasion you could freely explore the narrow and linear corridors that is the Other M map your exploration never resulted in uncovering a new item or a shortcut or anything like that. No, all items were on the clearly laid out path and you just got handed them with little to no fanfare or sense of achievement.
It was much more story focused like that of Fusion but it went past what Fusion had for the story. It gave explanations rather than adding new details.
I found it's "explanations" were for questions never asked and just left questions in their wake. At best it just went into detail with Samus when she worked with the Federation and what Adam was like. The thing is it could be summed up as "Samus was pointlessly rebellious when with the Fed" and "Adam was actually quite an asshole and we just erased any ideas of why Samus looked up to and respected him".
For the sake of understanding I ask that you explain what holes it made and/or left.
Honestly that link explains it all far better than I ever could. Off the top of my head there is how Space Pirates are retconned to lack sapience and are only really a galactic wide threat with Mother Brain controlling them. In Corruption the Feds only just managed to replicate Chozo tech in the form of the Aurora Units yet in Other M they greatly surpassed that to the degree that they could justify putting one inside an anime robot girl. How Adam pointlessly killed himself just so they could have a heroic death for him even though the station would just get blown up anyway. The whole "Deleter" plotline was a complete joke that didn't need to be there, was poorly handled and then later forgotten about.
There's the infamous line about how Samus hadn't worked with the Federation since she left which contradicts Prime 3 and in a way Prime 2 as well. Then there is how because it copied many elements from Fusion it invalidated the impact that those elements had such as Samus being surprised that the Federation was corrupt or that they were breeding Metroids. And how can anyone forget the Ridley scene that made Samus react completely different to something that she had experienced many times before and overcome.
There is a hell of a lot wrong with the game, the link covers it well enough.
After doing everything over and over to get rid of them and have them keep crawling back it's understandable to break down.
However it should have been gradual with signs of it taking it's toll on her. Instead we had her clearly able to react calmly and clearly then all of a sudden to fall apart. Heck Samus got so ridiculously emotional in Other M that they even retconned the way her suit works that it can't stay together if she starts blubbering. A major design flaw that has no reason to be intentionally added.
I wouldn't have minded the game showing the constant appearance of Ridley getting to her but I would have liked for it to be done in a way that matched her previous experiences and made sense.
I'll also point out that on a psychological level being near people you care about makes you more emotional.
Which brings up the point of why the hell would she care about Adam in the first place if he was like how Other M made him.
On a side note: The ship from Other M felt very reminiscent of the ship from Fusion. I may be imagining that but I always found them similar. This is unimportant though to the topic at hand but I was curious about your thoughts on it. Do you think they are similar or even the same?
Very similar, in fact Other M relies heavily on taking elements from Fusion as well as other elements from the other Metroid games for added nostalgia even when it doesn't make sense like Phantoom. The Bottle Ship copies the whole "Space station with a hub and several spokes that simulate natural environments from jungles, tundras, aquatic and volcanic zones" thing from BSL yet lacks much of the quality that BSL had. Heck they even copy the whole "Secret Metroid breeding lab that Samus has to escape while it is jettisoned into space and shows that the Federation is corrupt".