First, congratulations on a great game. This one packs a lot into one box and it does it well.
I have some suggestions that may be able to improve the game further, particularly in the user interface. My apology if I suggest a feature that is already present

- New Event window. Every thing that happens should be queued into an event window. For example, when one of your capital ships has its shields down. When you click on that event, it should take you to the ship. You should be able to set the number of events that are queued. 15-25 should be enough. It gives you an opportunity to attend to something urgent without having to struggle with the interface to get there.
- New Back and Forward buttons + History. You should be able to click on back and forward buttons to go to the last visited planets. Just like a web browser remembers where it has been. You should also be able to drop down an history gadget and pick a planet from there.
- Add Advanced fleet management with options to name fleets, attach fleet to planets etc.... I want my fleets to remember where their base is because I create balanced fleet and place them strategically.
- Add features to ships, such as auto-crossing wormhole. It drives me nuts when a fleet using auto combat goes through the wormhold and gets slaughtered on the other side because it has no support. I want my ships to be able to auto fight without crossing a wormhole.
- The Empire Tree needs fixing. When you start playing large games with multi-star systems, large fleets, I believe in falls short of a good interface. I am not going to get into it in details but it should not be scrolling when you are doing things and it should not have icons half visible at the bottom. Also, it should have a text version and smaller graphics. I suggest getting rid of it and replacing it with a global combat window.
- New Global combat window. This is something to pop using a function key. There is should have different views. One is the hierarchy stars->planets->fleets->ships view. The other is the fleet->ships close-up view. There should be 2 panes. Left is what you are looking at and right is what you can do. In the right pane for example, you should be able to move ships between fleet. You should be able to ping and even build on planets without going there.
These are a few features I would like to see. I'm putting this here for people to think about the user interface and some improvements. I know that the empire tree has impaired my progress. When I am in the middle of a combat situation with hot spots in 3 or 4 areas at the same time, I want more than fight the interface to be able to give orders.
Finally, the mega feature that I would like to see is scriptable ships and fleet. That's really a dream, but why not? You could write conditional instructions to your ships or fleet. In its simplest form, an instruction could look like this: if($this < $enemy)retreat. The bigger the game is, the less I feel like dealing with petty stuff. My attention is needed globally. We should be able to give general behavioural directions to fleet and ships. Different scripts could be written and stored, then assigned to fleet and ships. For example, the line of code above would go into a defensive script. Needless to say that scripted combat units would give the opportunity for players to go to the toilets during an online game

The makers of this game may consider opening up the AI and allow customisations. Have all the AI stuff in one file in a AI folder and prompt for which to use at the beginning of the game. People could exchange AI files on the net. That would make it more interesting. The default AI that handles combat for the human player should also be customisable.
While I am here, something needs to be fixed in this game. There needs to be different levels of urgency in the audio messages. I don't want to hear the dramatic "Our fleet is being attacked!!!" when one enemy scout is visiting a stronghole of mine defended by a fleet of over 20 ships and strong local defenses. That scout is going to get wiped out in a few seconds. Surely, the message should be proportional to the severity of the threat. I'd like to hear "An enemy scout is about to get fried!"

That's my 2 cents, I might contribute $2 when I have more time.
Cheers
The Peace Man