Probably everyone knows that right now, but still:
Pikmin change order:
These moves make the used pikmin to the last in row:
Fair, Bair, Up-air, Dair, Side-b (when/if it returns), Up-smash, F-smash, Grab (if it works or fails doesnt matter)
These moves do different order change:
Up-B: in the animation itself the used pikmin is now the one furthest from you away etc. but after the move order is normal again
D-smash: Used pikmin gets in front of you and gets 2nd last after the move, second pikmin in row gets behind you and last in row after the move.
With that order in mind, the options you choose may be dependent on your order:
e.g. blue-purple-red-yellow: you might go for a blue grab, a purple up-smash, followed by a red fair.
Regarding this, sometimes an emtpy move is also a possibility (or a low landing lag aerial before landing) just to change order as you want
EDIT: Down-b randomizes your pikmin order. If you down-b during a side-bd pikmin is coming back, it is randomized not last. If you do down-b too early, that pikmin is last. A newly plucked pikmin is last. See Oracles post... Messed up sth