Metroid Prime 4 Spoilers
So, the ending. The fact that they kill off all the Federation Troopers. It was quite jarring and threw me off for a bit. Especially since it's so unexpected, since they did fakeout deaths for the troopers in the last dungeon. It feels like an abrupt, jarring cliffhanger. And if you don't get the secret endings, that's what it is. The main mission is to escape, and while Samus does, the rest of the troopers do not and it's hard not to call that a failed mission. It's subverting expectations in the kind of way that drives endless, completely worthless internet bickering.
But if you get 100% scans? You get a bit more of Sylux's backstory. How he was a Galactic Federation commander who got all his men killed seeking glory, only to be saved by Samus's arrival. And then at the end of Prime 4, Samus has a team she has bonded with... And Sylux kills them all. Obviously, this is meant to make them even more of foils to each other. Sylux got his soldiers killed, Samus failed to save hers. And yet this context is totally optional.
And then if you get enough green energy crystals to get the memory fruit, you get a scene where Samus plants it. This was the prophecy that Samus fulfilled for the deceased inhabitants of Viewros. But all those Federation soldiers had to die for it. There's a certain cruelty to this. The prophecy was fulfilled, the chosen one succeeded, and others who had nothing to do with this were sacrificed.