Nice pano. Skies are definitely the toughest part of panoramas. Water reflections can be tough too. At this resolution I can't see too many of the typical pano flaws. Are you referring to the blown out area or the right? OK it is not as dramatic as the sky on the right, but I personally wouldn't expect much more given the vast difference in lighting.
How did you shoot? Now I have a camera I can control, I've found switching as much as possible to manual improves things a lot and stops the camera trying to "help".