My knowledge of single campaigns is severely limited so if someone already has created this campaign sorry. What if the Shivans never interfered with the Terran-Vasudan War and the war lasted until present Fs2 time with no side gaining any big advantage. You play the invincible Alpha 1 out to kick some Vasudan arse (or vica versa). Assume that somehow both sides have discovered shields, beam weaponary, flak guns, etc. I would think there would be a lot of new weapons and ships since anything Terran-Vasudan would be inapplicable.
Another question: If you could warp back to Fs1 and bring with you any Fs2 ship, fleet, whatever, assuming that the Shivans never interfere, what would you need to bring back with you to make the Terrans the absolute dominating force. Personally I think one fully equipped Hecate would do the job.