I do not use Navigation. It is useful, but not enough to sacrifice combat (and possibly colony) skills.
Only the last perk in Loadout Design 3 is good, but it is a doozy... well, more like mitigating a critical deficiency. The rest of the perks are generally useless because ships are so OP starved if I want any campaign hullmods. Without campaign hullmods, ships barely have enough OP, except carriers, who are extremely OP starved if they use anything better than Talons.
Electronic Warfare from the enemy seems much less common in 0.9, and it makes sense to min-max it today. In late 0.8, Electronic Warfare was common enough (among major faction fleets) that more than one point was useless because the enemy's EW offset yours roughly equally. Nevertheless, that first point is so must-have I consider the #1 perk in the game.
I only get Coordinated Maneuvers 1 for independence from Nav objectives.
Officer Management seems like a must-have if only to avoid paying the Reinforced Bulkheads tax on a lot of your ships.
Fighter Doctrine is (almost) must-have, more so in 0.9 than in 0.8 thanks to tweaked carrier and fighter mechanics that weakened fighters overall.
At least in 0.9, I have the option to have as many skills as officers and still have some for other stuff. Unfortunately for me, all of the extra points goes to colony stuff, because exploring and setting up a powerful colony is fun.
P.S. Now that weapons are guaranteed to survive as long as the ship survives, I consider Reinforced Bulkheads on ships mandatory, otherwise, I would reload the game the moment that ship is lost. (Blueprints are too rare to produce your own stuff until endgame.) Unfortunately, some ships cannot afford to spare the OP for that, and that is when I want the Officer Management and Fleet Logistics combo to remove that requirement. If I expect ships to die and stuff, Safety Procedures to reduce the clunker penalty, or maybe the other industry skill (either Recovery Operations or Field Repairs) to sometimes recover pristine ships as they are, look very attractive.
During 0.8, Reinforced Bulkheads was useless because weapons were still lost, and they were rarer than ships. Not anymore in 0.9.