I think that's the one thing that could save this entire set of issues and takeover of the comics, if they were dropping subtle clues and stuff in an effort to turn everyone on SuperDad, because he's going to be a villain eventually, but still having him be mostly the good guy and there being semi-reasonable excuses for everything, because you still want people to buy the Rebirth stuff and then be shocked when he turns on the good guys, but that seeds were planted and you kind of wanted to "boo" him by the point he really turns bad, and aren't offended.
I will go on record. If SuperDad turns into a bad guy, I will start buying the books again (Otherwise next week is my final issue as a subscriber, though I don't rule out buying an occasional issue if I have an itch or there's a good sale). Um, as long as SuperJon isn't then the new Superman or something- that's like the one way they could ruin that.
Imagine, though, SuperDad's just subtlety acting like a Superdick but still a good guy (Beating villains, technically doing the right thing overall) and people are defending him, but Batman never buys it and thinks he's not to be trusted no matter what good he seems to do. The Internet goes nuts and splits between people defending SuperDad and people defending Batman. Key battle, Batman is about to beat, let's say, a Kryptonian villain like Zod or H'el, but then Zod or H'el turns the table and is beating down Batman.
In flies SuperDad (Maybe this is taking place on top of a building or on a mountain or something- or in an office building on a high floor). SuperDad's in full gear, he's looking iconic, the sun is shining on the "S", his chest is puffed up, "This is a job for Superman (written in full stylistic font)" in a full page spread, floating above the ground with both competitors backing away. He turns toward the villian first and looks like he's going to attack, the villain flinches, then SuperDad turns and looks at Batman. Batman reaches for something on his belt. Full page spread again- Superman comes up and does his trademark Superman Punch uppercut to Batman. Batman goes down.
Zod or H'el approaches SuperDad with a wide smile "I knew you were on my side, brother.". Superdad pauses for a second, with an indecisive look, as if maybe that punch to Batman was just because Batman was going for something on his belt, but then smiles and says: "We Kryptonians need to stick together". They're laughing and smiling and clapping each other on the back. Zod: "Earth won't know what hit it". We see Batman lying crushed again, knocked out. From a distant vantage point, unseen to the adults, is Jon in his SuperBoy costume, crying, and then flying away. SuperDad, who doesn't see this: "Watch out world, THE REIGN OF SUPERMAN HAS BEGUN (New story arc)".
Then the next half dozen issues are dark covers, literally dark, like Superman in shadows doing various things, battling various people, with a sinister overtone to the artwork itself. We learn that he's not really from the Pre-Flashpoint main DCU, but actually a different alternate universe (But he is still the Superman of that different universe and a good guy there, just not as good as our Supermen have been, more a dick, so this is still a change for him, just less of one- also, that explanation saves us from having to hurt the legacy of the old post-Crisis Superman). He takes out every member of the Justice League one by one (Not killing them, but taking them out of the fight somehow). His own son eventually has enough and tries to stop him and Superman tosses him into the Phantom Zone and calls it a "time out for bad behavior".
Luthor is the last man standing to defend against Superman, and with Superman evil, Luthor of course must be good. He comes the closest to winning, but Superman wins, and for once we are sad that Luthor's plan was foiled. And Luthor just shakes his head sadly and says "I knew it. I knew it from the moment I first saw him.".
Superman and Zod rule the world. The governments surrender to them after they take out the world's militaries.
The media would go nuts with this. Superman is evil. He taking out Batman, Wonder Woman, etc.. He's turned on America. Maybe at the end of one issue, he burns an American flag and laughs. "Lies, Domination, and the Kryptonian Way" headlines the Daily Planet with a Lois Lane byline.
Eventually, new52 Superman comes back and kicks SuperDad's ass and sets everything right. He's the world's hero. He restores the flag and waves it in the air. He restores everyone's trust. He frees Jon from the Phantom Zone and finds him a nice couple in in Smallville who always wanted children, but never had them, who knew his parents, and he and Jon agree that Jon will use his powers when he comes of age, when he's ready, but for now his job is just to be a kid.
Some people would be very pissed, but these issues would fly off the shelves and gather big time media attention.
Then you return a good guy new52 Superman and make him very cool, modern, and edgy, with a 17+ rating and Wonder Woman at his side.
A bit more sex and violence than usual, and he drinks more ("I was dead for too long, now it's time to live"), but still the old Superman spirit and mythos. And you've got this huge audience to introduce him to. High collar and Kryptonian armor is back, as are red boots.
He and Batman and Jimmy, who's in on his secret identity, hang out and drink regularly. He's Clark by day again, but this Clark is cool. If he stops dating Wonder Woman he either hits on Lois suavely and gets turned down with a smile from a secretly loving it Lois, or Lois hits on him and he smiles and says "Don't you wish." but secretly admits to Bruce and Jim that when he's ready to settle down, he thinks it'll be her. Or, if the Wonder Woman thing goes well, he marries her. Maybe Lois marries Jonathan or something- or Bruce Wayne (Imagine *that* pairing).