Hello ! I know I'm late but I would like to add my little contribution :
First, the empire tree jumping around thing, this I remember, some time ago when I was playing on a kinda small screen pc, was really the one thing I found the most annoying about this game. Well maybe the lag was more annoying, but you could somehow avoid it by not playing too big games... I remember I stopped some games because I just couldn't manage to play with this thing jumping around at each click on a ship.
Now that I have a bigger screen, it is better really, but is still one of the most annoying things for me. SageWon said it comes from ships jumping between planets, I don't think this is the main problem. The main problem is simply when you click on something, the whole tree scrolls up or down, to place at the top the planet where the thing you clicked is at. Which is generally nice at the start of games and when you click on something outside the empire tree so it "highlights" where the thing is.
But then it becomes a problem when you have many things at a planet, well you can use stacked icons, but that way you can't really select things precisely... And for people with laptops or small screens it quickly becomes difficult to play.
Maybe it would be great to simply allow the player to toggle an in-game option like "prevent the empire from jumping". Keeping the default behavior until the player explicitly tells the game he wants it otherwise... And it seems so much of an easy fix, compared to other long standing complaints like the AI suiciding on starbases etc...
Then I also find it would be great to find some way so scouts don't blindly cross pirate bases, or more generally that the pathfinder avoids them if possible, but that's more of a feature request...
Also, a very minor 'bug' : sometimes I want a scout to go back and forth between two planets, A and B, so I queue move orders. Generally when you do that you want the scout to just appear at the planet and then return nearly immediately. It appears that when you queue the orders, if the scout was somewhere else than A or B (jumping or at another planet), then it does that great, but if it was at A for example, then each time it goes back to A, it insists on going all the way to the center of the gravwell, and then continues the queue, which is kind of a waste of time and can be dangerous if A is hostile... But this is really minor^^ just a thing I was thinking about that hasn't already been said.