I posted this in another thread, but decided that the idea merited it's own. Also, if this is already someone else's idea then I apologize in advance, but it's certainly new to me.
I preferred the old Ship Designer Upgrade button functionality although there are nice aspects about the "new" upgrade functionality. I've read in a previous thread that opinion is definitely split both ways on this. Some people preferred that the old components stayed on the ship, so as to only upgrade a selected few items. Others prefer the new way since they always upgrade everything.
Well here's an idea that might please both camps.
The Upgrade button could maybe leave all the old components on, but allow you to upgrade individual components by highlighting them and double clicking the new upgraded component from the list. Just like the colony manager, in fact.
This way you wouldn't have to remove an item unless you actually intended to do away with it. Fewer clicks, satisfies both sides' requirements.