The mouse controls are a bit tedious, but I grew up with them and I honestly can't play any other way. And I'd argue that they provide better precision, even if it is a chore to move around.
That being said, one of the things that made X-Wing (and even more so for Tie Fighter) great is the somewhat emergent gameplay. You are dropped into a scenario and every ship there has its objectives, which it will try to accomplish to the best of its ability. Aside from ships dropping in, very little is truly scripted. Again, this is more prominent in Tie Fighter due to the larger scale of missions (hell, some missions have secret optional subplots in that game), but still a factor in X-Wing. Combined with the fact that you're not flying any kind of magical superfighter, but rather a rank-and-file vessel goes a long way towards making you feel like you're actually a part of a (para)military organization. You are a soldier. A damn good one, sure, but a soldier nonetheless. And it felt nice to be just that, without the usual protagonist crap that tends to clutter games (I'm looking at you, Wing Commander).
All in all, a brilliant game, only surpassed by its successor, Tie Fighter.