Am I just imagining things, or in regular Sins didn't double-clicking on a selected ship select all ships of the same type?
I also noted that shift-clicking on the empire tree only let me add individual units, rather than selected the beginning and end of a group of ships.
Feel free to tell me I'm crazy, but I seem to remember these UI elements. If I am crazy, I'd suggest incorporating them, as selecting all types of ships in a gravity well is something I at least do quite often.