When ever I play a game that is not an RTS but do have RTS elements within I almost always find myself wanting more convenient control of my units, this is of course in alpha state so I never expected much in terms of commands. This game is a little more complex (has more potential to be more complex) than most RTS games when it comes down to the variety of orders. Placing too many Orders/Commands on the screen is probably not a good idea as it could just clutter things up to the point of unplayability.
Here is a diagram and viewpoint of how to implement more commands in this game without to much clutter. Note that this is just a base example and I was too lazy to do anything more complex using MS paint.

I won't cover what type of commands I would like to see just yet (past what is in the diagram), partly because that has been covered somewhat by other threads.
Let me know what you guys think.