-option to build certain buildings on all colonies ( late game planetary defense on 200 colonies isn't fun to build one by one )
-button to select all obsolete designs ( better than delete, because I'd like to keep a few, to manage multiple roles within same hull, so I'd unselect those first )
-checkbox to set a global option for new colonies "allow colonizing race only"
there were more, but forgot.. love the game, keep up with the tinkering

edit: my favourite.. an option to not get reports on attacks by monsters on civilian ships ( this specific combo, cuz these are spamming me so hard late game, that it's hard not to punch something )