This plot would probably make a good game, even without much added. I could see a bunch of people playing this game, thinking it's just going to be a glorified Challenge Mode from P1, and then run into tendrils of a cancer on the planet (or something. Maybe the Awakening Wood got taken over by the white mold with no Pikmin to kill it). It doesn't have to be organic, either, maybe some Man-at-Legs are forging a weapon to eliminate...
Well, I like the idea. The only real downside is that it might make it a little more difficult to make future Pikmin games if the main character, Olimar, is aging. I guess they could just throw in some prequels though.
Aaanyway... I was sort of thinking that Pikmin 3's plot could end up being about Olimar being part of a Hocotate program to start a colony on the Distant Planet. The collecting aspect of the game would be different building materials for different types of buildings. It would be drastically different, I know, but it was just my thought.
Heck, I'm not even sure if I like my own idea. I just thought it is a possibility! =P Personally, I like yours more TC.
Shadow Temple... Here is gathered Hyrule's bloody history of greed and hatred... - Shadow Temple Walls