Any One Still Playing This Game?

[Suicide Junkie]

The sliders/spinners from SE4 race setup. Far superior interface to use than a pile of checkboxes for +/-5%

Showing estimated time to completion on build queue items... NOT the time it would take if it were the only thing in the queue.
Throw in a small indication of how many resources have already been invested in the item too.

As an extension of #2:
Same deal with the flags. Make them 2D overlays, smaller, and pack them together so a sector with three races in it is understandable. A larger flag can be ok if there is only one race in the sector.