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How about (and this seems more plausible as it allows multiple games to be released allowing for more money) two games with the same story line, except Halo characters (either Master Chief or your own spartan like in Reach) are only playable on Xbox, and Samus and the Metroid characters (assuming you have a mode where you could play as a space pirate) are only playable on Nintindo's system. As for the universes being incompatible, in Metroid Prime 3: Corruption, we used a portal to travel to the ever distant pirate homeworld. Why couldn't we create another portal leading into the Halo universe?