Some more pet peeves:
Consistent toggle-click-policy, basically every mouse click (or keystroke) that opens a new UI element should close that element when clicked/stroked again. This already works pretty much everywhere but not with right-clicking parts, e.g. when wanting to quickly check a throttle limit or some such. It would be great if you could just right-click the part again to close the Parts Manager, instead of having to move the mouse across the screen to the Close button or to the app bar.
In the same vein, the top left "Burger" button should stay visible once clicked, so you can just click again to close the menu instead of having to move to the "Resume" line.
It'd also be great if the App bar were extendable with favorite apps.
Also regarding the app bar: the last (re)opened app window should be displayed in the foreground. Currently the z-order seems to be hardcoded corresponding to the order of the items in the app bar and app list, with the parts manager trumping them all.