The most annoying interface element in this game for me has to be "Do you want to upgrade this starbase?". A better approach would be to bring up the screen and then add a cancel button (yes, I know this could end up being a lot of work). The one idea that would halve the number of clicks I have to do for starbases.
Oh and don't ask me if I want to upgrade a starbase and then tell me I can't.