I can help you out with this.
First, currently the only way to select fixtures in Vision 2017 is through the scene graph, this actually helps quite a bit for performance, as making an object "clickable" adds another calculation to the rendering screen.
As for moving an Item, only conventionals can be moved with the arrow keys, if you select a fixture by it's unit number in the scene graph, you can right-click (cmd+click/2 finger click on mac) anywhere in the scene to focus a light there, then tweak with the arrow keys, or just move it the whole way with arrow keys. You can't use the arrow keys with moving heads as they only respond to DMX. It would be like trying to grab the head of a VL4k and turning it in a direction, it would resist, and try to stay where the DMX told it to be.
Software console: only conventionals make use of the software console. Personally, I think there could be a better name for it, the software console basically reproduces all of the physical options on a conventional, i.e. Gobo Index, Shutters, etc.
Lastly, the Root menu is designed to collapse after you delete something, it prevents the user from accidentally deleting more than just the fixture they needed to. We understand it can be a process to re-add it in the right spot. This is being looked at though, perhaps we can find a better way of doing this. As for the menu bar, what sort of monitor are you running Vision on? Or rather, what resolution? The icon size should scale per your display.
Hope that helps!