Oh these sound great! My knowledge of Gundam SEED is rusty, but the PLANT situation does fit this growing universe we're making more. The Archon Program would have been made for that expected invasion by the world's wealthiest people since governments would probably be too busy bickering with each other to be useful, which is another vulnerability and more reason for other colonies to defect. But yeah Earth and still-loyal colonies definitely would not expect to be fighting fleets of giant mecha. Communication between Earth and Britannia could have been getting less and less throughout the years, and they start to notice Britannia's growing ambitions and more colonies leaving Earth's allegiance, that's why they expected a war.

I like that idea that the Emperor and his circle being in secret contact with aliens (who could be a subterranean species to fit the Geass Order, hiding in Britannia's new homeworld. That way it's also easier for them to remain in secret for so long). The aliens could either be sowing division between humans by giving Britannia more support to be independent from old Earth, so that when Britannia and Earth go to war, they'll be easy pickings for them. Troy and Cornelia could have fought against each other a few times before the aliens reveal themselves, so they decide to join forces to prevent extinction and for these aliens to reach Earth. When they inevitably win, Troy can stay in the outer colonies to help them recover instead of going back home to Earth, and Cornelia can still remain in Britannian territory and help turn the empire over a new leaf so to speak.

How's that?