I've totally re-arranged my whole shiplist in the following manner: Frigates is now the TOS era, with everything from TOS frigates up to the Yamato BB. Light cruisers is TMP with ships arranged in the same manner, Heavy cruisers is all the TNG ships, and Dreadnaughts and BB's are whatever I want. Klingon and other races are set up similarly. Though you lose a little flexibility this way, it enables me to play skirmishes in whichever era I choose just by enabling certain ship types. I also have a more conventional, blended version of shiplist, and entirely TOS, TMP and TNG versions that I sometimes switch back and forth with.