After a short time I feelt quite comfortable with the controls...didn't had any problems...except that I sometimes wanted to just make my own waypoints. Still I could handle it quite well.
As for not finished features.
Anti shield weapons -> Depends much on the techlevel differance between you and you enemy. If your Anti shield weapons are week you won't have much of an impact on the enemys shields. But their are some realy hightech shieldbombs that have an area effect. These things are quite effective.
Pinpoint weapons to take out systems -> My favorite way to take out enemys. With a strong beams weapons you could easly disarm an enemy, criple its engine or do other things. I liked to dissable engines from stronger enemys, then I brought some distance between me and them and took out the smaller flys...or the other way around. Boarding ships and keeping them..or just rip them appart for stuff to be used would have been realy cool...thats a point where I agree.
Experiance-> Now that you mention it...yes it build up very slowly and the effect was very low. Could have been better.
The part that IMO mostly sucked was the sometimes dependance on luck. Still the story was nicely presented, the graphics great and the battles where fun to play. For me it had the right balance of difficulty.
And I didn't even know that it sold so bad.