I'm not a fan of the combat tree, as it's benefits mostly only apply to your current driven ship. Other hired officers can easily get the same abilities as you, and so while this tree might be useful to your piloted ship, I found it preferable to invest my points in other abilities which would have an influence over the whole of the fleet.
Rather than buff the current combat tree, how about making the officers under our command, have their skill effectiveness depend on whether we have the same ability unlocked or not?
The penalty could be a simple -% modifier on the current officer's skill
For example my officer has Powergrid Modulation Level 2, but I only have Level 1 unlocked. Assuming say a -50% reduction for skills I don't have.
Officer's current points in Powergrid Modulation (Level 2):
Before:
Level 1 - Flux +10%
Level 2 - +25% Flux dissipation rate while venting
After:
Level 1 - Flux +10%
Level 2 - +12.5% Flux dissipation rate while venting (-50% effectiveness due to having an unskilled commander)
It is basically a nasty nerf (at least early game); but I think it would definitely help pry a few points out of me to put in the combat tree.