Having played beta 2 for a few days, here are some of my thoughts. Apologies if these are duplicates of things already suggested.

Selected ships
A (optional, perhaps) box that shows what you have selected. Much as I like the idea of the empire bar, it has some limitations. Firstly, you are unable to see how many ships you have selected. Secondly, if you a lot of ships in a planet, there is a point beyond which the planet ships bar will not display any more. Secondly if you have item stack selected it's quite possible to select three different ships from three different stacks of 10, and have all the stacks highlighted making it appear you have 30 ships selected as opposed to 3. My proposal is an optional bar at the bottom of the empire window that will say what you have selected, for example:

Cobalt x 30
Sova Carrier x 2

This way you can easily see exactly what you have selected, without any guesswork.

Message options
At the moment the player gets flooded by irrelevant messages. Scout ships getting attacked? Yes, that's the whole idea. Scout ships incoming to your system? Who cares, they're not about to do damage. Ally under attack on a different side of the galaxy? You're not about to swoop in to his rescue.

There should be an options screen for messages, where you could select what feedback you receive. Options could include:

-disabling attack messages for specific ship classes, eg scout ships or noncombat ships
-disabling incoming ships messages for:
--specific classes
--combat ships below a certain total supply
--or if the system defences supply total are a certain % larger than the incoming fleet's supply total (eg, 30 supply of cobalts jumping into a heavily defended system aren't a problem and the user doesn't need to know. an entire enemy fleet jumping into your back yard are)
-disabling "ally under attack messages"
--except perhaps those that you actually have some hope of responding to, eg two jumps away from your planets or some such.

Hostile systems
Much as I love the refinery/trade ships, they're pretty stupid when it comes to choosing what way to go. They will always choose the shortest route, regardless of enemy presence. Their pathfinding should either be reworked to take enemies into account, or there should be an option when you select any planet to designate it as hostile, which would make civilian ships avoid using it to travel.

Diplomacy
I realise that the dimplomacy is probably still being worked on, but I would love a lot more diplomatic options, conditional treaties with break penalties, etc

Purchase options
The player should have the option of spending resources they do not have. The production would not start until the player has actually got the required amount, with the resource bar displaying red negative to indicate the game is waiting for resources to start a production. This way at least the player doesn't have to keep looking at the resources and hope to remember. Perhaps this could also be queued, so the player could run a several item queue to put their resources far into the red, then not have to worry about spending their resources as they come for a few minutes.

Subsequent to this, there should also be a production screen where all queued productions can be viewed, and dragged around to reorder/etc. Example, if the player has a few research projects queued and realises that he needs the ships queued after those first, he could hit the productions screen button, and drag the ships to the top.



And lastly, this isn't much of a bug, but it's the only one I've noticed so far: since the resource values are stored in floats and rounded for display purposes, it's possible to have the game display the requisite amount of resources for a purchase, yet be unable to purchase it due to the real value being lower.