If both of them got to the onion area at the same time before you had time to get pikmin out of the onions (which is doubtful), then it would be a nightmare. Otherwise, Waterwraith wouldn't be much of a problem, and the Smokey Progg could probably be taken out with white pikmin (assuming they're immune to his toxic waste).
Currently playing: Final Fantasy XIII, Final Fantasy Tactics, Final Fantasy IV: The Complete Collection, Radiata Stories, Persona 3: FES, and Pikmin 2.
Meh, don't take Waterwraith out of its cave. The whole point is that the cave's designed around it with passages just fit for it and sublevels without purples. As stated by others, if you already had purples, it's no problem, as is Submerged Castle's final sublevel.
AngelTails: pretty sure the point is that the cave is going to be harder with yellows, so it doesn't exactly matter how (s)he got them in there.
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