Probably a crap idea, but how about something like this:
The penultimate boss features the player battling Spacegodzilla, King Ghidorah, Mechagodzilla and Destoroyah, with the order you fight them in, and the number of them you fight depending on the number of players and the difficulty setting. (ex. Hardest setting with one player, fight both Ghidorah and MechaG).
Eventually, a nuke, or some other weapon explodes, fusing the four monsters into a gigantic chimera...thing, that towers over the player's (or players') monster(s). After getting their ass(es) kicked for awhile, another nuke or weapon explodes, granting the player monster(s) a super mode (ex. Godzilla--> Burning Godzilla/Super Godzilla, Mothra--> Armor Mothra), allowing them to fight this Final Boss on even ground.