i think this is intentional. Since some abilities are very strong when you can ignore the cooldown, like anomaly in 3 spots, or bulwark in 3 spots. It would allow you to spread the cooldown out between them.

This is definitely intended.

The duplication of skills is intended to allow you to have different passive runes selected to use on the fly in middle of battle. You can have one for single targets and one for clearing maps for example, say, AOE for clear and damage for single targets.

It is NOT intended to let you play Bleeding Edge piano.

I assumed this so I hadn't even bothered with duplicate skills... but I saw a video of someone using triple phantom blades.

Not a cooldown but gaines charges over time... so essentially with the extra charge he had 9 charges instead of 3.

I'm wondering if thats intended. Not as strong as some skill with a much longer cooldown, but still neat nevertheless