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Don't forget about Co-Op in the main story itself... my brother and I were pissed to find that despite having two captains in the main campaign of Pikmin 2, we couldn't both play it at once in co-op.
Another mode I thought of: Defend the Onion. Waves of progressively more difficult monsters storm the onion, leaving you with only a bit of time between waves to grow new pikmin and get flowers on the ones you already have. There can be a competition version, where each player is on their own but facing the same types of monsters and seeing who can last longest (maybe cherries can be collected to get extra monsters to attack your opponents,) as well as a cooperative mode, where... well, you understand how that would work.