The point is that pikmin can't do -anything- without a captain, other than grab/attack what's in their immediate proximity. At least that's how I see it. Notice how you always find pikmin right under an onion in Pikmin 2
Smoky Progg is the best optional boss ever Deal with it. The human race sucks ass sometimes. - Doktoroktopus
^This. Pikmin have tiny brains, they can only fight/ pick up/ dismantle/ build whatever's within a three foot (Pikmin sized, not our size) radius when they arn't being commanded. To have them run to the Onion woul totally destroy that point.
---A wise man once told me that the secret to a long life is to keep breathing as long as possible.---
Not only would it be too easy, but it would basically make the "left behind" risk nulled, removing a strategy from the game.
If you're telling them to do this, then they were already with you and the left behind was irrelevant.
To clarify, I figure it would have all Pikmin currently under your command (is there a name for that?) head back to their onions on the same route they'd take were they carrying something. As far as interaction, they'd act as though they were with you, and not idle, meaning they wouldn't stop to grab things or attack enemies.
Majora's Incarnation is what happens when game designers smoke crack.