Hmm. Lemme think about this one a bit.
I see what you're saying in terms of the problem, for sure.
I'm going to noodle on it a bit and see if I can come up with a more clear-cut solution: people unaware of the system would probably wonder why they were seeing a cooldown of 3 on a 2-turn cooldown ability. I've been tempted for awhile now to consider trying out tying Cooldowns to Speed... and I've also been trying to get rid of "speed up cooldown" passives and replace them with "reduced cooldown" passives for unrelated reasons but that hasn't been a high priority I admit.