I don't know if you guys noticed it, using USAgent's Herofiles, my Superman couldn't stand against Doomsday any given time that I gave up fighting against him and chose other weaker villains. When I tried to fight him again just for old time's sake, I discovered that when I move Superman behind Doomsday, the hits get connected and he wasn't able to block nor dodge those hits. When I go face to face against Doomsday, I couldn't even land a solid hit with decent knockback, but when I hit him from behind, I get to knock Doomsday from his feet. I just run around in circle, hit him from and then finally won for the first time.
Did you guys experienced this?
I think that usually happens when "inactive" isn't checked in the characters Passive defence, but I just checked my Doomsday Hero file and it is checked and I fought him in the rumble room with my Superman and he was still blocking my attacks when I was behind him so maybe yours is unchecked.
I got my Doomsday with a 50% passive defence which is pretty high for my hero files, I'm not a big fan of passive defences over 30%, but I think he should be able to shrug off 1/2 of the attacks anyone can dish out. I have Doomsday more powerful than Superman because I don't feel Superman can take him one on one. When Superman beat him in "the death of superman" Doomsday went through the Justice League before he even fought Supes. But you can always lower his defence or up the damage amount Superman does if you don't like how the battle plays out.