I appreciate the fact the there is runes to upgrade skills but I think it would be even better for the personalisation and gameplay if they have more impact. If there is more runes which modify the skill, like the one on fire ball where they stop explode but go throught enemies, or the double Beam.

I understand the meaning to put "small" runes like more damage or reduce cd. I agree it had something.

Maybe some "Big" runes point and "small" runes point could be a solution. Or something like that.
I haven't play enought to know if it is possible but the fact that all runes aren't available in the same time is a good thing too I think.