It is not counter intuitive and it works as it is supposed to. If you're learning something new you are going to be picking up a lot of things quickly at the beginning but as you get closer to mastery of that thing the longer it takes to make small improvements.
The leveling system is also designed as such to promote concentration in a few key areas, they do not want your character to be a god at everything and frankly that's how I prefer it too because it provides replayability and I think that is simply good role playing design.
Your learning rate goes down with levels which means that especially when your learning rate is at the highest you should be focusing on the things you want to learn the most. You can keep your learning rate pretty high if you pump a lot of attribute points and learning points into a specific area.
The problem is you cant shut off skill gains on skills you dont want to raise.
If you manage to get any of the party support skills you intend to use a companion to cover up a few levels before finding a companion for them because you accidentally spotted a hideout and gained a scouting level, or engaged in combat against looters and took a little damage and gained a surgery level then looted a few different food types from them and got a steward level, that is forever lowering your potential maximums. If you participate in a tournament and get 10 levels in some weapon you are not building your character around, that is forever lowering your potential maximums. Those few levels can then go on to be the difference between making a perk breakpoint or not in your main skill before the learning multiplier totally 0s out hard capping you - possibly hundreds of hours down the line in the save.
That is not a good design because it actively encourages you to avoid raising skills you dont want to focus on. So it encourages you to rush to find companions early while avoiding raising any skills and reloading if you accidentally do. It encourages you to avoid tournaments entirely. dont want to raise trade? You better not sell things at all because now in 1.1.0 you dont need to make a profit on things you have bought, just selling food looted from bandits will very slowly raise it.
When you come up with a character concept, building that character now requires constant obsession and checking to make sure you do not accidentally raise a skill you dont want.
It becomes even worse in the long run because even among skills you DO want to use, focus points and attributes only take you so far, you will be leveling your primary skills outside of learning bonus in 'the end', and in this case, maybe you only want the 200 riding perk, and want to dump all your remaining learning potential into getting your weapon as high as it can possibly go? What then?
The system as it currently is could be somewhat salvaged if you could just toggle off certain skills from ever raising. This would still leave a system were players would be pushed to try and snag some level 25 perks early on, becaus etheir player level pushes the 2 attribute non focused learning limit below 25 (it starts out at like 44 if you raise only that skill from level 1, meaning you could probably, for example, have 2 in vigor, and only intend to raise focus points in one weapon type, and get the other two up to 25 before they hardcap if you focused on it early on)
Is it good for a games system to encourage players to have to twist in such ways with so strict a playstyle to simply use the character progression system optimally? In a well designed game optimal use and intuitive use are the same.