Perhaps level ups should be tied to a general XP score that you gain from killing foes, winning battles, training (passive from the Leadership skilled companion / main character with a higher level), doing quests, and generally being successful (trading for a profit, etc. etc.).
Those level ups give you attribute points and focus points as they do right now.
The skill points are gained by actually applying the skill.
If we separate the level ups and the skill points from each other, then we would erase the strange situation of "If I want to raise my skill cap in X skill, I have level up. In order to get another level up, I have to gain more skill points, so I need to use skills I do not want to use / learn." In my opinion that would make the current system much easier to use, because we would get more focus points and attribute points to pump into the skills we actually want to use, without having to worry about acquiring tons of skills elsewhere to get the level up in the first place.