Here is my idea. Have a "Fleet by Class" Rally point option. I like to keep my transports and my Military ships in separate fleets. In rally point management it would be great if the game would have a "Fleet by Class" option along with current "Normal" and "Fleet" options.
Sort the constructors, transports and military automatically into there own separate fleets within the same Rally Point.
Save a lot of time sorting when you want them separate.