Robson,
I cannot tell you which is better, to kill the transports or to kill the destroyers or to kill the battleships. I do know you have to make decisions on what you are going to hit because you just dont have enough to kill it all in the first round.
I FEEL if you are going to try and get London early, then you really want to kill both those transports in the first round. Perhaps get one of the two battleships as well (SZ 111 is easier than SZ 110 due ot the number of fighters that can scramble.)
I FEEL if you are going ot try and get Moscow early, then you really want to kill the cruiser in SZ 91 and at least one of the battleships, preferably both. Other ships are gravy (like SZ 106.)
However, it is your game, play it your way.