These are some general suggestions I came up with for interface improvements based on my most recent 14 hour game:
When placing an item that overlaps another structure, instead of canceling the item construction and playing the message, just play the message (leave the item selected for construction) so that we can just click another location.
We need an option to toggle on our fleets to cause them to auto-attack the same target or to auto-attack the target of a designated lead ship. This way they focus their fire on one target until it is dead.
Using the scroll-wheel to zoom in and out while the cursor goes over a selectable object causes "zoom bouncing" (the zoom level bounces back and forth between two different levels of zoom).