Of course the game cannot have a challenging curve if everyone can do everything perfectly fine all the time regardless of their skill choices.
My colonies are hugely profitable, because no matter what I skill I can slap full AI cores on them from the start, since they are easy enough to come by. While I am doing that I am perfectly capable of exploring to the deepest edge of the universe with an actual capital fleet. Of course raiding half the core worlds that basically have non existant defenses I can do aswell.
We are already allowed to respec, so it should matter more what you are actually skilled in.
My fleet doesn't care if I am combat oriented or not, because my officers certainly are and they come in droves aswell.
I overspent a little? Oh let me just quickly queue up a couple of 2-300k bounties that are always readily awaiting for me to go there and slap them and for my convenience they are also straight up next to the coreworlds anyhow.
Put more of the basic functions behind skills to begin with.
AI core useage - technology
Availablity of 100k+ bounties either reduced or they are much deeper in space.
More than 2 officers? Leadership
Colony upgrades? Industrial
Stop being so gentle to the players, because it makes the skillchoices basically uninteresting.
It might also be worth a consideration to unlock some aspects only if you have e.g. both skill sides unlocked. For example AI core useage could be 5 in technology, but if I also want to get the redacted ships, then I need 10 points in technology and thus making sure, that I am struggling somewhere instead of how it currently is where 15 levels equal 3 of 4 trees like common.