It's probably too early to tell, but I wonder how long it will take people to essentially combine both games into one. Say, multiply a Star Destroyer's stats by 10 and then just run it in the game for fun? I know after playing a handful of games, it'll be very early on my list of things to attempt.
In one of the Transport missions, there's turbolaser fire coming in from 'off screen' (ie. 'off mat'). I think that's an interesting concept in a way.
I do like the idea of integration, but I suspect it will require us fans to come up with a regime of mechanics for it.