My first impression is positive, even if the upgrade price was a little bit high. I like Ara integration and it seems that melodyne is working very well. Ok for color customization and browser. Very, very good are the EQ zoom and the tape simulator!!!
I still have a problem had on X2. If I click on any part of bus console, when a waves plugin is inserted on, sonar freezes. I just posted this to the support. I think that if I clean X2 from my pc everything would be solved, but I don't want to loose the x2 featured plugins no more in x3...

Waves are also VST3 all of them, did you keep the setting to let X3 replace with VST3 on the fly when opening old projects?
 
Just thought it might be handled a bit differently.
I try to reproduce here and come back.
 
As I understand - no gui visible on Waves?
To me it sounds like a graphics driver thingy - I would check latest drivers for graphics card.
 
I stayed up until 3.30 this morning(europe) exploring that fantastic X3, coming from 8.5.
I must congrat Cake for a job well done.