One thing I would like to see would be a 'spacer' or 'reserved space' component. This is a box that is basically free and exists to take up space. I can think of several uses:
Building a ship to size, where you want to save some space for future improvements.
If all but one component of a ship is researched, and you want to get started, you fill out the space with these, then lay down the ships. Partway through construction, the research finishes, and you retool the yard (if necessary). Then, when the ships complete, you refit them to the new sensors. There are ways to do this today, but they cost more.
When you wish to slide a ship past your overlord's approval process, because they restrict what you can build, but not what you can refit. (This one is probably pretty specific to my current game.)