Oh, a level editor would be awesome. In Warcraft 2 I always had fun making "narratives" in my maps... (like in one, I had a sort of puzzle where your starting base would inevitably be destroyed in a short amount of time after the level started, and you had to use your peons to cut through or sappers to blast through a forest on one side to make it to your smaller expansion base to rebuild).
I can see a similar sort of thing with a level editor in Pikmin. And it's possible, for sure - heck, they did it in Brawl, so the precedent has been set.
Hey, how could they balance having some urgency with the ability to roam and explore to your heart's content? Maybe have the first part of the game be urgent, then you can revisit levels to find treasure later on after the urgency has been dealt with...?
What happens if Olimar gets a rival? Another spaceman crash-lands on another part of the planet and discovers Pikmin and their loyalty too, but he doesn't have benevolent ends in mind like Olimar? Hmm... maybe this is starting to get too formulaic... could still be an interesting angle, though.