Transparency amount should be user-configurable, with 2 sliders, one for Start Menu and one for Start Screen. User choice is paramount.
You can pin nearly anything to the left pane of the Start Menu, by simply dragging it there.
Your theme syncing "approximations" are wildly incorrect. They sync a lot better than you portray.
For your examples:
Selecting "Teal" on the phone correctly makes Windows 8.1 select...
Improved? I can no-longer immediately "Like" posts I see in the "What's New" page.. I have to wait 5+ seconds for an app to load. I don't know if I'm sold on this concept yet.
The final link at the bottom also says Beta, but shouldn't, right?