I solidified my thoughts on cooldown during the D:OS 2 kickstarter, before the EE came out. The EE has indeed greatly improved the issue of cooldowns.

I am not a fan of tying cooldowns to abilities and skills at all, though, because it makes it harder to balance. Under your system, a skill could have a cooldown reduction of between -2 and 7 - a spread of 9 turns! That's EXACTLY the kind of thing which creates balance headaches, and why I don't like it.