With the Apr 2017 release (detailed here: https://kb.blackbaud.com/articles/Article/109686 ), assessment skills can now be inactivated. They also have an amazing new filter interface that lets them be sorted based on where they are in use, among other features.
Several additional ways I think they could be improved further:
A filter for grade plan too.
Being able to add new skills within the Grade Plans in the School year setup tab would also make this process more user friendly.