About Beyond Good & Evil

alienprotagonist - revealed at the very end with no earlier indications of it.
starship - can be considered a spoiler as well, for it is not expected nor indicated by anything for the first ~1/3s of the game. Nor is it exactly obvious that you'll be manually flying around with it.
moon - this is pretty obvious as soon as it's mentioned, which was somewhat early, IIRC. Visiting it happens at the very end, though.