I guess they won't change the clouds before they develop a new weather system. The problem with the rotating clouds is not exclusive to Aerofly, you can see that in P3D, and I'd reckon in Xplane, too. The only solution would be to have real 3D volumetric clouds instead of the 2D sprites we have at the moment. But this probably would be quite heavy on performance. The new MSFS 2020 seems to feature volumetric clouds, and I'm really interested to see how it looks there and how big of a performance hit it will be.
It's not just me is it?
No, it does look awful in VR at certain altitudes.
You can sometimes improve things by changing the height of the cloud layers.
I might be wrong, but it seems to me that the cloud height doesn't adjust depending on altitude of your starting point.
If you have the clouds on "middle" height its super noticeable at high altitude airports, and barely noticeable at near sea level airports.
