well, honestly the only main difference that can't be solved/bypassed between the 2 game engines is just how the fighters rotate: in fs2 the ships turn in a predefined amount of time, no matter the speed, in xwa-xvt the rotation time depend by the engine output. This is a bit important, since it affect gameplay and could be a major issue for multiplayer.
Other minor differences are how ships hyper out and in(but it is only a graphic effect), the AI (wich isn't a problem), the possibility to track down and destroy any warehead class, the warehead AI, collisions. But they all are really minor issues.
Oh and there are also all the beam types. Some can be simulated (stealth), some other not, but since I'm a purist I really never liked beams, so I'm not going to cry for them.
Most of the other differences doesn't exists anymore: in SW ships are far smaller, but with the zoom this isn't a problem anymore; virtual shields can be setted for capships (althought without graphic effects); we have system disruptors simulating ion shots(wich is probably better than how official games handled them).