I've tried X3 with 2 good flight sticks, and I wouldn't recommend it - the game is really geared towards mouse control. Even space battles are a problem, since all fight is done at too far a distance for a joystick to be convenient (not precise enough unless you'd get really close, and you'd be dust before you'd get close enough).
[LONG, please bear with me, it may solve the problem]
I couldn't disagree more!
I've played both X2 and X3 on CH Flightstick pro (until it died) and Saitek X52 and I couldn't imagine trying to play X3, especially a modified X3, with mouse only. Here's why:
1. Joystick / throttle combo is far better handling multiple concurrent controls with acceptable precision, read: changing the pitch/yaw while adjusting the throttle, strafing left/right, changing targets and shooting the main gun array. While it might sound far fetched, it's more-or-less required if you want to survive heavy guns fights, especially on highly modified X3's. (X3 with XTM, RRF and a touch of rebalancing)
2. Keybaord mapping: On the X52 I used a software of my own creation (sourceforge'd) to map large number of key combos to the different buttons on the joystick and throttle. This is more-or-less required if you want to master item 1.
As for the subject at hand (targeting enemies), well, a couple of things:
A. X3 includes a rudimentary physics model. While far from being real (Ships behave like aircraft instead of free-space fighters), both ships and gun fire are effected by this model (E.g. shooting while banking will spin the gun fire, much like corner kicks in football) making unaided aiming (see below) very hard. Especially when you're still flying a light-weight fighter, fighting other light weight fighters.
B. In order to "solve" the problem, you simply dock at the nearest equipment dock, and buy a "Fight Command Software" Mk1 and Mk2, this will not only give you a calculated hit-box (which more-or-less mimics modern fighters "pickle"), it also gives you some level of gun-fire-aiming corrections (Controlled by the "k" key). Just to clear, this is not a cheat, this a part of the game; Computer controlled fighters are either equipped with it (and nail you from 3KM) or not (and miss you from 20m). -Do not- trying to enter a gun-fight without one!
Beyond that, beyond the well documented issues with LGP support, X3 is an -amazing- game.
While the base game is no better than X2, the -huge- amounts of extensions, modifications and scripts (let alone the ability to customize the game yourself) that change each and every aspect of the game makes the best game I ever played, bar none. (...Even my wife agrees)
On the down side, X3 is a very steep learning curve. It has a fairly complex economy model and technology curve, making it far from ideal to anyone looking for a point-and-shoot space shoot-em-up game.
However, if you are willing to spend the time (and the frustration) required to master this game, you'll understand that the only thing more satisfying than killing 10 enemy fighters and getting 10,000 credit reward is to command a fleet of 20 battleship and 10 dreadnoughts and let them clean one of the Xenon or Khaak sectors gaining a 100,000,000 credit reward
P.S. I don't work or affiliated in way to LGP.