Where did you see any evidence that there are bigger ships, to give you this impression ?
I just wonder why you'd call a 'Light Cruiser' a flagship like Pike did in the first film?
Because flagships are not always or even usually the largest or most powerful ship in any particular fleet. Strictly speaking, the flagship of the U.S. 7th Fleet
wouldn't even classify as a light
cruiser and is half the size of the supercarriers under its command.