I think multiplayer could work, with the proper design.

My idea:

The person or people hosting the game would be stuck playing as the mother brains. Only in MP they could survey the entire battlefield whenever and they would be the only ones capable of sending in a purchase for more units/weapons.
everyone else would be soldiers/vehicle pilots, etc. you get the idea. Plus there would obviosly be many different modes of online play besides that, depending on ones preference.

The only problem with MP is supporting a server(s) and having the hardware capable of processing that stuff. Think the nuke mods make your comp lag now? wait till some idiot n00b hacks a server and tosses one during a match and crashes the whole damn thing.

Otherwise, I say MP is a given!