I have noticed a few things that I hope are in the process of being fixed; as I don't have time to look through all the previous posts and see if any of these have been mentioned. Anyway, the first (and perhaps foremost) is the auto-launching of new ships: I hate that! I prefer to launch the ship in the direction I want it to head; and (at least half the time) it tends to end up being launched on the wrong side of the shipyard.
So, with that in mind, I have a suggestion: Make a few changes to the Shipyard! As it stands now, the shipyard is rectangular and only displays the ship currently in production. What if it were hexagonal and showed up to five ships in production with the sixth slot being where the next ship to be finished launches from? Then add to that the ability to rotate the shipyard so that the ship is launched in that direction upon completion.
If you really wanted to get creative: you could set it so the five slots represent the five ships produced most often and have the center display the ship currently being produced. The player could then just click on one of the five slots to show which ship is to be produced next. The possibilities here are almost endless; as a lot can be accomplished from the main screen without even opening another window.
And... Speaking of windows (sort of), I come to my next annoying item: The ship display (on the right side of the main screen). I trust that the ability to sort by size, name, etc. will soon be added... But! I'd also like to see the scroll bar moved to the left (rather than the right). Why? Well, in the process of trying to scroll down my sizeable list of ship, there's a little pop-up that ensues. That's not so bad; but it remains there even though I've moved on to the scroll bar (unless I move all the way off to the right and come back to it).
I'm also having an issue with the ship designer; but that might require a post of it's own.