After thinking about it a little more, it seems to me that the only skill really worth putting 9pts in is probably Starship Command, as that would give you that extra 1% boost (compared to stopping at 7) to your hull, speed, and maneuverability, regardless of the ship you use throughout the entire game. Of course, this is assuming that +18 means +18% and not something else. Also assuming that it would give the 1% boost to all three of those attributes and not divide it up in some way that would lessen the effects.

As for all of the other skills, I'm having trouble justifying any more than 7 pts and any less than 3 or 4.