It's a tough call - omnipotence and omniscience would drown out everything else and Moore definitely wanted to say a thing or two about Superman. But yes - he's imperfect. It makes sense to me when I consider him as a newborn god pretending to be human for shits'n'giggles.
I can see that. However, the one thing that sets Manhattan apart from Superman, is that Superman is a bit of an oaf, whereas Manhattan's obtuseness stems from his inability to empathize with the human perspective. I suppose the same might be said of Superman, but I'm not sure that Manhattan ever fooled himself into believing that we has connecting. My superhero experience is limited, but I always felt that Superman was a guy that convinces himself that he cares more than he does. Building such a spectacular timepiece palace on Mars seemed like something that would interest someone connected to time and space, and at that point, it felt out of step with his evolution to me. Manhattan's shrinking outfit was a brilliant metaphor for his loss of connectivity. I would think that the place he brings Laurie to on Mars would either be just some weird cube, or someplace built completely for her benefit, like her living room. I'd prefer the weird cube, since he wasn't thoughtful enough to remember her need to respire. I dunno. I appreciated the nod to his past with the watch-making pieces, but going that route, he should have made the whole of Mars into a clock.
Frank Miller's take on Superman was that he was Lawful Good but didn't care much for introspection. He was black'n'white and not particularly deep about anything, which made for superficial success but not much else. Doctor Manhattan, on the other hand, is kind of a true neutral - he's aloof from everything. Manhattan's constructions, to me, had a lot in common with the bizarre assemblages Lem talked about in Solaris - things that had no discernible purpose, but that clearly reflected an intelligent hand.