Justified Expectation of Pleasant Surprises
If I may hazard a guess, it seems possible that the game designers' intent was to make interacting with the setting and the challenges fun, mysterious, and rewarding, not the power increase itself.
Let's say, for example, that this game has some string of abilities that, a few notches down the road, gives you the ability to leap much higher and farther. It's not immediate, but you can see that following this particular branch will give you that capability. You file this away for future reference; you're more interested in pumping your gun abilities for now.
Later on, you come to a location in the game where an enemy stronghold has a poorly-guarded back entrance... that's 10 feet off the ground. You realize, because you had a list of options to look through, that you have the ability to pour some skill points into these Athletics abilities and obtain the jumping ability needed to get through here. However, you've also been coming across a number of locked doors that a few points into Lockpicking would get you past... which do you choose? Each has its own potential for surprise and reward, and skill selection is just a tool for exploring that space.
I think the goal is to be up-front about skill choices and their repercussions because discovering those skills isn't supposed to be the point of the game. The point is to play the game, gain a feel for the challenges you encounter and your preferred methods of dealing with them, and then pick skills you KNOW will support those methods. The pleasant surprise is in encountering new challenges to test those skills against, not in randomly discovering that you can fly now because you picked the right 3 abilities.