Morph Button.You can save multiple Blueprints for the same ship, and pressing the Morph button will switch the systems on the ship to the Secondary design. This would cut down the need to switch out systems manually, or for the lazy, allow one ship to do multiple jobs.
Think, Robotech/Macros etc.
Battlegroup Attack.You should be able to link several of your fleets into a battle group, and then when you want to attack with this Battlegroup, just click the Battlegroup button instead of all the individual fleets.
Sometimes I have 20 fleets in my stack, all ships there for specific jobs, it becomes a pain to do missions with all the extra fleets out, and expensive to keep cycling them through the Reserves option.
ANother option along the lines of the Battlegroup, is to register several of your Fleets to Attack mode, and just by clicking on missions, Bases, Encounters etc, those fleets would all attack.