Enemy: Meklar fleet rating 490,000.
Me: Mrrshan fleet rating 1,200,00.

Battle took place at a military outpost.
I lost all 16 titans. Meklars lost 3 ships.

Something way wrong.

You had 16 titans and your rating was only 1.2 mil? Sounds like your tech rating was not very good and or you had heavy fighters on your ships. Fighter bays in the current build are not populated and therefore they do zero damage.
Did you auto-resolve or fight it out?
Auto-resolve could very well end up with this result, but it would not be the norm. If you manually fought this battle the design of your ships would dictate the results. Shields can make a huge difference. Missiles have a high power rating, but I have noticed in fighting manually beam weapons do better because of a couple issues. One is if you do not have dauntless guidance and you have mostly if not all missiles for weapons then you might launch enough missiles to kill the first target 10 times over, but the excess damage will vanish because the missiles do not re-target. If you do have dauntless guidance then there is what I think is a bug in the game in how missiles re-target. The leftover missiles seem to re-target the last ship in a stack and take a round about path to the next target and then after they kill that target they lock on to a ship at the start of the group and take a round about path there. The result is the missiles ping pong back and forth killing their targets much slower than what I think should happen all the while the opponent's beam weapons are chewing you up.