I'd say it's Sylux' ship. He is part of the Federation's history, and is a good idea for a villain.
And on the Dark Samus front, I say yes. Ridley would be fantastic, and I have every hope of him being playable, but I would still love to play as Dark Samus. The moveset potential is amazing, no way a clone.
And my thought on the Aurora Units/Mother Brain? Assuming I'm thinking right in terms of chronological order, I would say Samus' report on Mother Brain, and the assumption there are other Chozo bases with abandoned Brains, I would say the Federation reverse-engineered the idea for themselves.