I can't make sense of the skill slot restriction

Top tier builds don't need more skill slots. Hell, they don't even benefit from it.
Meanwhile, if you're engaging a lot with weapon swapping, then 9 gems total, with 2-3 gems for spirit gems, leaves like 3 gems for each weapon. That's severely lowering my creativity.

I agree. It would be nice to add them or not limit them at all. And then remove rings without a stone from the game as useless.