Far be it from me to voice the name of true evil, but I liked the system that Star Wars: Galaxies used for their ships. You, as the designer, 'built' the ship from the ground up. It could hold x tonnage, and you had to decide if your ship had faster engines thus losing weapon or shield power, or both. In the end, the loadout of the ship was your decision. This IMO was roughly akin to a ship's Chief Engineer tweaking the specs of a class ship to meet the demands of the Captain and crew.
I also liked the way you could program the ships computer/droid with various tricks to switch shield power, weapons power, give the engines a boost, etc. You could almost hear Scotty thru the comm yelling 'She's canna take any more sair, mah wee bairns!!' and whatnot.
Let's make it diverse yet uniform. IDIC, as we all know.....=)