Really the targeting system leaves a lot to be desired. There needs to be a bigger difference between what a ship looks like when it's targeted and when its not. Also an arrow pointing you in the direction of what you have targeted would be nice for hectic space battles.
Finally, the targeting system doesn't seem to always pick what is closest to you, it should, and it would also be nice to restrict the auto targeting to something within your field of view. So you don't target a ship behind you, ping it with your weak aft phaser/distrupter and spin around looking for it for 5min.