I would like to see something that runs in the FS engine, but that plays like something totally different. Something that feels not exactly like the lucas arts games, but also something that doesn't feel like flying a GTF Perseus in the shape of an X Wing.
Weaker fighters will have a lot to do with this, as will more emphasis on jinking and less on Countermeasures (actually, the absence of CMs will mean major modifications to the aspect seeking nature of the missiles, or it will simply be too hard). And, of course, without beams it willbe hard to confuse the game with FS2. But still, the way things are done should be different - cockpits, for example, are a must, as are fiddling with the flight dynamics majorly between ships. A replacement for the afterburner will also have to be given (presumably by shunting up the max overclock speed dramatically).
As for the campaign itself, well, that'll depend on the ships we get made, of course. But I'd like to see more than just open space battles. Atmospheric missions, if they can be done, would be nice, but not essential. Making very, very rare nebula missions but fairly common asteroid field missions would be a good way to go I think.