Think of it as specialization. Previous games had major and minor skills, but in the long run this division meant nothing. Now it has an impact on your game - you can't master every single skill, you need to focus on those most important to you. It's similar to a class system except you're not restricted from using non-class skills, they'll just be less effective.
And if you still feel uncomfortable with the new system, you can use the legendary features and keep levelling up until you attain all perks you want. It will be incredibly boring, but the option is there.