How about the following options:
I play another game totally unrealted to this called UFO:Afterlight. In that game you can turn on and off certain alerts, and change what you want to happend for each alert. Applying this technique to this game I came up with something like the follwing:
For each alert you would have several options like if you want it to be a verbal warning, just or just make the little Icon for its respective report flash or even if you want the target of the alert to appear in empire tree. So for example that whenver a planet come sunder attack I would get a verbal warning, the little icons in the lower right that log verious events would flash (well only the appropriate one) and the planet gets added to the empire tree. The only roadblock I ran into is how long they stay on the tree.
The solution I came up with is to have any unit or planet added to the tree that is not a currently selected unit appear with a check box next to it (or something like that). When you no longer need it over there, click the box and BOOM, all gone.
This lead me to another idea. What if you could add planets or units to the tree at will? They are still context sensitive like before, add a sun, and all the planets you know about appear below. These planets would also have checks, so if you own a bunch of planets in one system, click the star, add it to the tree, then expand it and remove whatever you don't want there.
This lead me to my final idea. Tabs. Lets stick a couple of tabs at the top of this new tree. Maybe like... 3-5. I could have a tab for each system, or one of planets I own and planets my ally owns. Or some of my enemies.
The goal of this overhaul is that with a tree such as this we could all make it however we wanted. Making it look like the default tree is as simple as adding all known stars, you get everything. Also if your resolution is crappy, having tabs keeps you from having to scroll, allowing you to view everything with a hotkey (yes the tabs should be hotkeyed
) or 2 instead of clicking in scrolling.
I realize this might be a lot to code, but its the best solution I could come up with and the only one I think meets everyones requirements regardless of play style. Let me know what you think and suggestions and critisism are always welcome!
Edited because I needed to clarify some stuff in the beginning. Oh and dont turn this into a UFO: afterlight discussion, I just used it to try to illustrate my point (if your familiar with the game)