An onion could be an overlord, since it floats and has tentacles to act as supports. A spire could work too, maybe a greater spire.
As for blue pikmin, maybe zealots? They seem watery... sorta.
As for parts, you could use a lot of things. Various terran/protoss buildings should suffice.
Crashed ship = crashed BC structure, naturally! Maybe increase its hp as it gets repaired to show its completion status.
Enemies could be anything really, just make it unique.
OH OH IDEA JUST CAME TO ME!!
How about you use the three worker units (probe, drone, scv) for the pikmin, and have vespene/mineral based powerups as the food token things that you can bring back, and they make more pikmin for you! Use zerglings/zlots and the like for maybe bud & flower pikmin?