Manhattan doesn't seem all powerful. Definitely seems below Mxy.
But he also seems to be learning, adapting, and has basically no form. Hence the problem with comic characters, we've seen so many Gods utterly tank anything the humans put out that you can't write a God that is currently ignorant of what he faces, and write it down to a more reasonable level. And I'm a big fan of grounded portrayals to get the story out, but the featsters won't like it.
But I will say that if he maintains this portrayal, it will be hard to put him above the Mxys even if they hammer us over the head with it. Grounded portrayals of omnipotence be damned. Comics have gotten so oneupsmanship that if you don't play the game, your message gets jumbled. Though I do think that little itch in the back of our heads with the Myx/Oz thing would have been better if it never happened. DM comes out of the blue to DC with no prior interaction for example. We could have reasoned DM from Watchmen could have done what he's done instead of the New DC Manhattan who's the best ever.
srug
Also funny how Doomsday Clock opens up like a house on fire when we do finally get to the one thing everyone wanted at the start; Dr Manhattan.