Awesome! If you've ever seen Gundam SEED, I think a PLANTs type situation could work here where instead of Britannia fleeing Europe and conquering America, they could have left Earth several generations ago to colonize outer space. Saying that there was limited to no communications between Britannia and Earth would still leave us a lot of room for discovery. Maybe we could also say that tensions on Earth had been high for a very, very long time with the world leaders operating under the expectation of war/invasion. Even with all their preparation, none of them anticipated the Knightmares, however.

For the enemy, what if we do aliens and we keep them fairly loyal to how they are in your setting while also using them to represent Geass and the Geass Order? Say that the aliens had been secretly supporting Britannia and only the Emperor and his closest confidantes knew. Maybe either the aliens decide they don't have a use for Britannia anymore and indiscriminately target humanity, or Cornelia discovers the truth (likely after something severe happens and is brushed under the rug) and starts to rebel against the aliens (though not necessarily against Britannia itself).

I don't know! Thoughts?