As for Zeon and the PLANTS, I was thinking that yeah, considering both of them are at war with the Alliance, they could form an uneasy partnership considering the circumstances. However, it'd definitely be uneasy, it's not like the PLANTS agree with Zeon, it'd be a mutually exclusive relationship.
Merging Machine Island and the Dark Continent actually sounds like a good idea, so why not.
I see Saotome Labs and Axion being rivals more than partners. Considering Axion is owned by a rich kid.
Well, which one did you want? I get what you're saying, to emulate the games choice of "real" or "super". However, I created Crowe for the express purpose of tying the plot together in order to get all of the characters eventually in one place. I don't mind compromising a bit, though. Which type of original did you want?