I have some actual ideas for the "MGS3: Subsistence" style of subtitles. You can make fun of my ideas, but you better offer some of your own, too.
Metroid Prime: Impact, Fission, Fissure
Metroid Prime 2: Abyss, Rift, Reflections
Metroid Prime 3: Termination, Infection, Invasion
For Prime 1, Impact from the meteor that starts the events of the game (and the Impact Crater location), Fission and Fissure also from that and from the radioactive effects of Phazon. Fission in particular has an issue with being too close to Fusion, but hey, the original game was released at the same time as Fusion, so there's some history there.
For Prime 2, the plural in Reflections would be important so it's not too similar to the ideas for Corruption, and because Echoes was plural. If you tried to pluralize Abyss or Rift I think it would sound worse, but those are probably still better picks than Reflections. You can't really use Rift if you use Fissure for Prime 1, though.
And I don't really like the options for Prime 3, but it's tough when "Corruption" is already maxed out on edginess and most synonyms sound goofy or have other connotations (degradation, degeneration). Infection might be too medical-sounding, and both it and Invasion are a little too on the nose. On the other hand, Termination is a whopping 4 syllables. Probably some room for improvement here.
The first game could colloquially be called either "Impact" or "Prime Impact" and the other two would be referred to like Echoes and Corruption are today.