The treble does open up somewhat after some burn in. But, I also encountered the same problem that people are describing here of the highs being somewhat 2-D while the rest of the sound is 3-D. The culprit in my case was my flat screen TV. Once I moved the Omni's forward a good foot, which put the speakers about 2.5 feet from the TV, the problem was fixed. So, positioning is important. The more space the better.
Also, w/ the stock Omni's, I found while I loved the sound for music and for TV, for HT, I felt the central image was too diffuse for my tastes. Adding a center channel speaker solved the problem for the most part, but I found I didn't have any problems once I added the Skiing Ninja crossovers to the X-Omni's. The resolution improved considerably, and I didn't have the problem any more. Of course, haven't had the problem w/ the O-3's either.
As for the Omni's being "dark" in comparison to the Neo's and Ref 1's, I can see where you're coming from, though it isn't the description I would use. The stock Ref 1's are somewhat bright and etched, and the Neo's have a more forward presentation than the Omni's. The Omni's are more spacious/3-D and laid back, and they don't have the detail of either the Refs or the Neo's. Danny's omnidirectional designs are never going to be "in your face".