The flashing effect every few seconds across the entire bar as you use skills needs to go. Flashing is used to draw attention - I have no objection to an important skill just off cooldown flashing (e.g. Whirlwind), or a skill that only enables under certain conditions and thus requires attention drawn (e.g. Riposte), but not the entire hotbar.
The cooldown itself is ok, although on long CD skills it becomes hard to spot if they have become available, because the availability indication of skills is still very hit & miss at best. A proper visible timer or countdown, or instead of a horizontal dropping bar, make it a circle that turns around, would be better.
Above all, make these things configurable!
Stop assuming you know how everyone wants to have their UI work. I don't mean total UI modding, I just mean that if you decide to implement some new UI feature that could be made optional, make it optional.
Pretty sure it's always flashed. It has at least always shown the global cool down over all the skills and this always flashed. This isn't new, the only thing that was added was the white border.