This technique doesn't allow you to pick specific things for specific actions (e.g, selecting a structure to scuttle).
Heh, that's a pretty circular argument.

I'm saying add a scuttle button elsewhere, and you're saying it's already there. I said elsewhere damnit!

Perhaps there are empire-tree functions that I am not aware of, but scuttling is the only thing I could see using it for. You can access all your build queues and planet management by simply clicking on a planet in the main window; you can access all of your fleets...
From what I can tell, the only reason you'd want to use the empire-tree is for Scuttling, and for selecting an individual ship that isn't currently in a fleet. Am I missing anything? Seems like an awful lot of UI space for such a narrow feature set.
Hold down ALT, it gives you the names (as well as lots of other info).
My whole argument was I don't NEED to know the names - I know what the planets are! The volcanic planet, the green star, the blue ice planet, the planet next to the L shape... They don't need names in my head.

It sounds like you aren't aware of all its functionality or you would prefer to use the Selection Based Empire Tree, which has much different behavior and is likely more suited to your play style. Check it out by activating it in UI options.
I just checked out the selection-based one, and my god I'm so happy. It's so much better because it de-clutters my screen. However, I am still curious as to what purpose it serves, other than scuttling and individual ship selection?
Assuming there is a use for it, the lists get neigh-unmanagable when you have a lot of ships in the region, is there a way you can break the empire tree down into ship- and structure- sub-tabs?