Superman: Make Superman's secret identity slightly more plausible by having him shun media attention and simply focus on saving lives. As Superman, he'd be more like Lois' guardian angel than her boyfriend. Metropolis would be a fictional version of the real life Metropolis Illinois, the expansion and urbanization of which was spearheaded by Lex Luthor. Lex is a billionair scientist and buisnessman who's expertise is in electronics, engineering, and computer programing. He's made Metropolis into the perfect city by secretly controling all major aspects of it, like the police, the city government, and even organized crime, and killing anyone who says otherwise. He has long term plans for the rest of the world, his main focus at the moment being the middle east, and eventually plans to run for president. He initially tries to get Superman to work for him, and succeeds in doing so, but Superman cuts all ties with Luthor after seeing the skelitons in his closet, and they become enemies. Most of Superman's enemies exist or are present because of Luthor: Metallo was a hitman for Intergang who was turned into a cyborg by Luthor to kill Superman, Bizarro was created to kill and replace Superman, The Parasite got his powers in one of Lexcorp's illegal genetic experiments, Toyman was a serial killer groomed by Lex to target organized crime figures in order to keep them in check, and Brainiac came to Metropolis to use Lexcorp's resources. I would minimize the presence of Kryptonite greatly, and have Superman's villains either match him physically, outsmart him, or have other powers that level the playing field. My biggest change would be, simply to not be repeatative, have Zod and that crowd be the leaders of a small band of Kryptonian refugees who come to Earth seeking a home, and then tentiones quickly flare and escalate into violence.
Batman: At the very begining of his crime fighting career, Bruce wouldn't be all that effective. He's just walk around at night, scare the **** out of people, and every now and then beat up a mugger or rapist and tie him up for the cops. It isn't until he starts secretly working with Dent and Gordon, and starts playing up on the fact that he's a detective, that he gets anything accomplished. I'd minimize the revolving door aspect of Arkham by having villains like The Joker get caught less often. I'd also portray The Riddler as a fairly compitent, albeit manic-depressive and OCD, criminal mastermind who is a thorn in Batman and Gordon's side, but as he sticks to thefts and con jobs, is fairly low on their to do list. The villains Clayface, Copperhead, and Killer Croc would have been normal (although in Croc's case, deformed) Arkham inmates who received super powers from the experiments of Dr. Hugo Strange, and Kirk Langstrom, simply for the sake of making him less of a rip off of The Lizard, would have been a physician at Arkham who found out too much. Carmine Falcone, Black Mask, and The Penguin would be recurring characters, and Gotham's biggest crime lords. Maxie Zeus would be the leader of a cult/street gang. Dick Grayson would have been closer to sixteen when he came under Bruce's wing, and Bruce would have trained him more because Dick was going to be a vigilante regardless, and he wanted to make sure he didn't get killed. Bruce's three main teachers would have been Ted Grant, Henri Ducard, and Ra's Al Ghul (Bruce initially thought he was merely an eccentric billionare, not a terrorist).
Wonder Woman: Themyscirca would be mainly the same. The mystical nature of the Amazons' physical prowess and longevity, and Wonder Woman's powers, would be largely debated by the rest of the world. Diana's main foes would be figures of Greek mythology, and more political and/or militaristic types, as she would encounted corrupt leaders in her role as ambasadore, and would often volunteer to aid U.N. Peacekeeping forces and keep the troops in line. She would also be a major political activist, and quasi-spiritual figure in the sense that she freely talks about her spiritual beliefs when asked.
So, yeah, basically the best ideas from Greg Rucka's run.
Martian Manhunter: I'd have him have been on Earth since the 1850s instead of the 1950s, mainly because I love doing flashbacks, and play up on the idea that he doesn't just have one secret identity, he's got hundreds all over the world. He'd be even more mysterious than Batman, and the source of interest for some of the more fringe cosnpiracy theorists, occultists, and UFO enthuseists. He also has ties to many of the other characters, serving as Clark kent's history teacher and a member of Diana's Embasy staff, as well as having ties to Lex Luthor. Not that he trusts, likes, or agrees with the man. He simply adheres to the old saying, "keep your friends close, and your enemies closer."
Green Lantern: I'd keep the partner system the GLC has now, and loose the yellow weakness entirely. I'd also ditch Parallax and the other color coded emotion pokemon things. Hal and John would be sector 2814's GL's, Guy would be a member of the GLC's black ops devision, Kyle would be Ion, and for the sake of simplicity, I'd have Alan Scott be the former holder of a possition very similar to the one Kyle holds now. He'd be the hero cop who's pulled out of retirement for "one last case." Sinestro would be a dirty cop who was kicked out of the GLC, and his personality would be modeled after New York gangster Willaim "Bill The Butcher" Poole. Hal and John would be part time members of the League, as theyr duties as GLs keeps them busy in space.
The Flash: I'd have Barry's ID have been public from fairly early on, although not right away, as he would have had a hard time juggling his secret identity with his police work, and it's just easier to have it all be on the department's time. He'd have been Central City's hero cop. I'd also state that his power is, at it's core, the ability to absorb and manipulate kinetic energy, which obviously lends itself largely to super speed. The Speed Force would be a bit more mysterious, with a lot of people initially thinking that it's just Max Mercury and Savitar spouting mystical mumbo-jumbo. The Rogues would basically be the same: a bunch of thieves who used mostly stolen technology to up the ante in response to a crime fighter who can punch you at 500 MPH.
Aquaman: I'd play up on the mystical nature of Atlantis, and have the Atlantians be, at least partially, mystical in the nature of their existence, being similar to gods and other mythological beings in the DCU to an extent, and have Atlantis be an amalgamation of every sea going myth every to be conjured on the Atlantic. Orin would be much more interested in keeping his people isolated from the outside world, and his public status would be down played.