The only way to speed this up slightly is to zoom maximally into a void zone on the main map, and don't trigger/click anything else anymore.

Still, processing will take time, esp. if you're playing gigantic all-abundant maps. Quicksaving and reloading might also be an option, as the game does NOT clear out old information from the RAM, thus, longer games will proceed ever slower.

However, you'll loose some income/influence each time you reload - although this can be countered by doing anything which will change the influental environment on the map (ie. leave one planet's colonization for the ending etc)