I'm still thinking that Weapons and Energy skills can be simplified into one skill with multiple layers.
For instance, why put 9 points into Auxillary and Weapon performance when the returns are so small? Why not just make it X Performance, and the more skill points you put into it, the more efficient your power levels are and your performance rises at the same time.
or maybe just engineering: hull repair, energy management ( balanced between shields and weapons) without 10 items that are all designed to boost energy to: more energy (aux modifiers), shield power , weapons power .. Even it ment adding an additional slot for engineering consoles (to chose how to best spend or boost energy) .. that might help manage it better.
One area that might be interesting to see developed a bit better would be engineering REPAIR with matching BO skills (not just the skills of the player).