Ugh, skills for Elite kind of game. That would be tough indeed... The core poblem is that's an "arcade" game (you fly the ship, aim and shoot), and for these games artificial skills (no player's skills) are usually not working that well...
Well, in our case it plays like EVE in 2d world. So, there are a good number of skills actually. The problem is making it into a coherent system... which is hard.
I guess I was not much of a help
Well, anything helps