Haha, that hadn't crossed my mind. At the moment I typed that, not putting much thought into it, I had only considered it for using it to move around Olimar (which, admittedly, wasa bit dumb). That would be pretty awesome.
However, I think they could do something really awesome on the top screen, something other than just a map, too. Something to add another layer of depth into the game.
And maybe you could say certain things into the microphone and the Pikmin would do something. Not directions or anything, because that would be a pain and ineffective, but after every stage or something you'd get a certain word or sound to say, and when you said it into the microphone the Pikmin would do something special. Maybe just some fun, funny acrobatics, maybe something actually useful but that is used in particular situations. Could depend on the level. Just something extra, for fun and maybe be useful.
Just thinkin'.