I actually think it's fine as it is, sure, there are a lot of skills one probably doesn't take, there are enough skills that you need to focus on a few, I think you can only max out like 6-12 skills if you play to the level cap.
As for skills you don't want to take, leave those to companions. Also, I'd say the medical skills are all pretty important.
I'd love for them to have modders be able to change their effect, as it is now most of them are in the engine.
Also, one thing that's been bugging me. Yes, it's petty but it's still bugging me, the corpse limit of 150 is for me only about 76, for the next game, if something says the limit is 150, then do please make it 150.