I only have issues with a few cooldowns.
The cooldown on Tornado is definitely excessive, that one could definitely be cut in half.
I also don't see why Rain has to be 6 turns long, considering the effect ends after the first turn. I think that one could be cut back to 3 turns. That would give it better synergy with The Global Cooling-Ice Breaker combo.
Running out of skills and needing to use regular attacks is only an early game thing. Later on you will have more skills and will have lots of options to use before your first choices come back off of cooldown. I don't see that changing. If you want more skills available, put more points into Memory early.
I completely and totally disagree with the idea of tying cooldowns to "having X attribute above a certain threshold". That makes it harder to balance. Before DOS 1's EE came out, I argued against tying cooldowns to intelligence because it made hybrid characters worse, but hybrids of that type don't exist at all in DOS 2 for different reasons.