Pokemon and Digimon aren't even remotely the same. So I'll have to respectfully disagree.
<Snipped quote by Double>
The thing is, that kind of setup is anathema to ambiguity, which is the theme that separates Gundam from shows like Macross. The very idea is that you're sometimes going to end up liking the antagonists and thinking the protagonists are bores or douchebags is critical to the show. I think that by creating a third party and using them as a main faction, that treats both canon factions like equal evils, goes against one of the things that's been a theme of Gundam for forty years.
<Snipped quote by Double>
At this point, to be completely honest, I think we'd be cutting out all the reasons to play a UC-based Gundam game. And actually F91 was set around the Federation, just not including Zeon. The Federation was just really weak and borderline unrecognizable by the time of F91, and there wasn't much of a focus on the fact that the soldiers helping Seabook were from the Federation.
But I digress. The point is that cutting out the conflicts between Zeon (and its derivatives) removes pretty much all of the defiining aspects of everything up until the Late UC era. And the alteration of the timeline needed to make it fit really takes away any incentive to use the UC. If you're choosing to make a game that doesn't directly involve the setting's actual conflicts, then there really just isn't a point in using that setting.
It's several unnecessary leaps in logic to explain why there are no Gundams for the PCs yet, too; Gundams were not at all common. They were all very limited production, if not completely unique. There's no explanation needed for why we don't have any, because it's not a given that we would. We're just not in a situation where we would have any.
But given the sort of setting changes you guys would seem to want, it honestly seems like it would make more sense just to craft an AU whole cloth.
@DisguisedDemonThat's... Not in Build Fighters