I love the idea of making them "source empower-able". I think it would fix both issues ... In any case it would be sad if the system remains as it currently is, because I would like to be able to use these skills. Right now, I don't even buy them because it's just a waste of gold and Source Points. There is no fight that is unbeatable without using a source spell (afaik), so why use them at all?
It would, but it would also introduce the Problem Of The Larian Skill Designer Going "what the fuck do you mean 'we need to figure out how to empower 160+ skills'? AAAAAAAAAHHHHHHHHHH!!!!!"
(Plus Skill-crafted skills? Nah, we can let them off and say crafted skills can't be empowered.)