What about not allowing the player to design their colony initially? Instead of allowing to make a helicopter, all the other cells can slide around the players cell to form a sphere. When the player unlocks the multicellular editor (with much more than 5 cells, maybe a hundred or so), he or she can start with an already three dimentional ball shape (the playthrough can still be 2.5d though). After that the evolution can follow steps similar to embryogenesis.