I'm no UX expert and I definitely do not have the image of the completed game in mind.
However, production screen and ship design screen are completely different things.
Production screen needs to be streamlined as a player visits it really often, up to multiple times per turn.
1) After a planet is developed, there are three empty squares in the upper row - factory, lab and planetary defenses.
As autodevelopment is the way to go:
1.1) planetary defenses may be included into autobuild queue (with expansion once the tech is available)
1.2) manual "factory", "lab", "farm" buttons may be replaced by "development profiles" in a separate UI element (even to a drop-down list)
2) idle behavior ("stockpile", "trade", "research", "auto") can also be moved out into a separate UI element (again, even to a drop-down list)
3) idle behavior choice should be remembered and applied immediately after a player's order (like ship or a... ship) is complete
This way these lavish tiles are reserved for player's creations, for starbases and ships, and both colony-essential behavior modifiers are moved out (and are, preferably, accessible from the production tab at the main map).
Ship design screen, while somewhat counterintuitive, is better than StarDrive 2's and is far, far better than GalCiv 3's.
As a player goes there with the intent to indulge into some creation, it's ok as it is.
Filtering out all incompatible modules from the list after clicking on a slot may be a cheap and effective improvement.