Gentlemen -
Here's a few things that myself and a few other regular RTS players have found grating with the interface and unit handling.
First, its really difficult to tell the range of defensive structures while placing them. Could we get an overlay as to their range (similar to PA or SupCom) that is both accurate and adjusts to terrain? A similar overlay for radar would be nice too. 
Factories need a stop and pause command desperately. Please don't exclude either of those. If my eco tanks because of a raiding party, I'd rather not cancel all my build orders just to pause the factory. Also, can you let factory rally points take queued commands, just like units? Pathfinding isn't bad, but sometimes I wish I could tell my units to go over this hill rather than around it when coming out of a factory.
There's no set 'max' size for armies on the ui, but I run into this max size all the time, especially when a dread is leading the army. At around a thousand units i cant add any more to the army. Speaking of which, can we remove the completely arbitrary 'one dread per army' stuff? Late game I have tons of dreadnoughts, and sometimes I need two in the same spot. Sometimes (Proxima, I'm looking at you) I need four or five dreads in one spot. It would be nice if they would work together.
Lastly, what's the end game? There is, of course, the victory point system, but no explosive or awe-inspiring way to obliterate your opponent. After a certain point, players and AIs become so entrenched that assaulting them is a daunting prospect. It usually devolves into one side throwing themselves against the others primary defenses and just getting slaughtéred again and again, even with more control of the map.