Well, after all most games are commercial projects using which you have to feed a lot of people(investors, programmers, designers, composers etc.). Therefore you cannot expect them to present really serious and deep stories, in the way authors are able to do personally in literature. Therefore trying to interpret too much into the story/taking them too seriously mostly won't get you anywhere. There might be occasional strokes of excellence but in general storywriters for games were just rushing to meet deadlines. In this case, bringing back the last Meteor could be a touching story, however for the sake of commercial production they couldn't really produce a coherent narrative for it across all Meteor series games, and in the end Samus just ended up being a self-conflicting and basically brainless and senseless character. Yeah, games played at certain stages might bring deep nostalgia, but those most likely come from personal experiences instead of the stories themselves.

By the way, quite a remarkable story in terms of personal experience.