I've always thought the Unlearning system was really flawed, people don't want to throw away something that they already put time into.
Here I am with a 1800% learning time penalty because I don't want to spend hours throwing away hard-earned skills just to learn new ones faster, and if I end up spending 2 months learning a new skill in the future then it'll just push me away from the game rather than act as an incentive to unlearn things.
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This is my suggestion for a better system.
Lets say you have a brain capacity of 30, this should mean that you can select 30 "main" skills. Main skills have no penalty. Any other skills have a small fixed penalty, like perhaps having Mining 4 would have 40% more energy used.
This scraps the current unlearning system, so you're never told to throw away skills, and the learning time penalty would either be scrapped or severely reduced. The big difference here is that once you learn something you have it permanently, and instead the skills outside of your brain capacity have a small-ish penalty
The way you select/deselect which are your main skills wouldn't be too different from the current unlearning system, but I'll reiterate that you're never throwing away skills entirely which makes a big difference.
Edit: To clarify this is effectively the difference between unlearning skills to simply learn others faster and unlearning skills to upgrade the ones you use the most, with the added benefit of not making you throw skills away completely.