For one or two games, I did not take Navigation because I wanted three more skill points for combat skills. Eventually, I got fed up with bringing extra tugs and tankers, not to mention crossing pulsar beams repeatedly because pirate bases kept respawning in neutron star systems, and eventually got Navigation.
In my latest game, I did not want to take Sensors 1 because I wanted the skill point for something else. Eventually, I had a pirate base bounty in Penelope's Star that I spent thirty minutes trying to find, but could not. Usual tricks to find the base ended in failure. I grabbed Neutrino Detector and it revealed the base hidden in the outermost asteroid belt, too far from planets, relays, and other stuff that are usually close by. I consider Sensors 1 mandatory for the rare times a pirate base spawns in an unusual spot that makes it almost impossible to find without neutrino detector.
Most of all, I like colonies, but not pather cells, so I spent nine skill points in Industry solely for colony skills, and considered Planetary Operations in Leadership for the stability bonus (effectively +1 colony). After finding out Pathers were bugged, I felt buyer's remorse because those points wasted in colony skills ended up gimping my combat power (because points I wanted in combat went to colonies because I also wanted to be a space lord with a big empire). Alpha cores are unlimited (provided the Nexus is left alone to spawn unlimited Ordos), but skill points are not. No respec makes it worse.
At least next release will have respec, although Alex wrote there may be individual exceptions.