There may be a lot going on in your empire, but there is plenty of warning for key events. Vocal alerts and large event buttons warn you when your empire may be in trouble or experiences an important milestone. At the top of the screen, a large flashing research, diplomacy, or pirate button will let you know if your research is complete, if a player wants to engage in diplomatic relations, or if bounty is placed on your head! Portraits of other players will also flash on your screen when they have an offer for you. Planet and ship icons will flash red when they are under attack.
While most of your post is valid craig, I feel this needs to be addressed so people don't get their hopes up. The vocal alerts are a very poor way to rely on warnings on your empire. I generally play massive team games with allies (AI, no multiplayer, the general populace is too immature to play a game like this online), and my allies messages seem to take precedence over my own. I can't tell you how often I have lost a high level cap ship because there was no audible warning that it's shields were down (at least not until it has 300 health) because my ally was under attack because they were flying through the pirate base and the "big icon" was replaced by another telling me my allies attack force was under attack while it was attacking an enemy planet or something silly like that. Even when I don't have allies, my trade ships keep going into enemy territory and I get messages that they are under attack every 5 secs. I've lost planets and last minute bounty wars because of this too.
Also, the research icon flashes when your researching anything, at least for me it does, not just when something is completed. As soon as I start queuing up research it starts flashing. And I've never seen the "underground" button flash when bounty was put on me, only when a pirate raid is being prepared.
And I personally think the empire tree is cumbersome and the search engine is missing things that should be added (and by should I mean the "duh" type of should), but this last part could just be me.
Other than that though I agree, I like the fleet system, although i would prefer if they moved as one unit rather than just all the other ships following the lead ship like puppy dogs. And the zoom is nice too, I actually find I use the zoom and quick jump (double tapping a control group number) more than the tree.