Custom Stat Skills:

Why is it that only some of the skills do damage using STR / AGI / INT and not all of the skills?

Balance's sake.

Pretty much that. But I'd add that in some cases it just doesn't make sense. Time Mage's innate teleport, for example. I guess you could have its max distance scale off int or something, but unless it gets big enough to reach from Lothlorien to Kalm, it's kinda pointless since it's still limited by vision. I'm sure if I went through every skill I could find more cases.