When Kid Flash says that 'The Justice Society isn't truly lost', it's kinda accurate; since many of the JSA members are actually in Earth 2, and it's implied that there ae older counterparts still around, if elderly. So there could be a hint to whats to come.
Wally needs to get out of the Speed Force and he is dragged out by someone who is close to him. Reminds one of a certain scene from Justice League Unlimited...
The Reveal that Dr. Manhattan from the Watchmen is behind the New 52. Why does this make sense? There is a lack of hope. The Watchmen are from a world where super heroes with the powers of Superman does not exist. The costumed heroes are either killed or forced into retirement, the most powerful man is a pessimistic being who has lost all hope, their most intelligent hero turned evil and psychotic, their gadgeteer member is a washed up has-been, and their best investigator is an Axe-Crazy sociopath who has lost touch with his old self due to tragedy. These are people who wouldn't get the idea of the main heroes inspiring hope even in the worst of moments, and also shows why the heroes act so different; with Manhattan removing 10 years, he removed certain hope spots that kept the heroes optimistic and mostly looking at the bright side despite tragedy.
The ending of Action Comics #958 seems to strongly hint at this, as Mr. Oz is watching the fight between Superman and Lex Luthor with Doomsday. Doomsday is about to kill Lex, leaving Superman in a position to either let him die through inaction or put himself in mortal danger to save his arch-nemesis. Oz says, "Think, Kal El — what will you do next? Only then can I make my move." In other words, heroism and self-sacrifice vs. Machiavellian pragmatism and self-preservation. Sound familiar?
In Titans Rebirth, Wally just needs to zap his friends with a little Speed Force. While people think this is a Deus ex Machina of sorts, it actually makes sense; the Speed Force is a universal force powered by what looks like electricity. All it's doing is zapping their hippocampus with what Wally knows and it helps fill in gaps that Manhattan left behind.
If one realizes something about Lex, it makes sense why he'd want to be more heroic if this version of him is a good guy; he's grown to LIKE The role of a hero over being a villain. Is he an egomaniac still? Yes. But now he is more in-tune with the heroic game because he's been Darkseid once. He likely wants to forget it. Plus Clayface is a hero in Detective Comics and it could be the case with Cheetah helping Wonder Woman in her comic, so Rebirth could also be reformation for some of the villains that they had fought.
So, now that Jacob Kane has been revealed as the leader of the Colony, it's obvious that the Colony had been in development for years, and he even says as much when he tells Kate that her Batwoman training was intended so that she could be a part of it. That means that all the way back during the events of Batwoman: Elegy, Jacob was secretly involved with the Colony. The brilliant part is that it all makes sense. Issue #937 of Detective Comics reveals that the basis for what would become the Colony was already being developed about six months after Kate was kidnapped, and shows that even back then Kate expressed a desire to go into the military, a path Jacob was obviously pleased with. And why not groom his own daughter for a high-level military position? Kate's dismissal from West Point threw a wrench in those plans, and he dropped them for a time. When Jacob finds out about Kate's first outings as a vigilante, his word choice indicates that he's not a fan of Batman, and when Kate defends her actions by invoking the Bat symbol and what it stands for, there's a beat panel, maybe indicating that Jacob is considering getting Kate back into the Colony, who would've at that time been more explicitly Bat-themed. Kate then goes away for two-to-three years to train, plenty of time for the Colony to begin operations and recruitment. Also, remember that while Kate was inspired by Batman, she didn't try to copy his look when she first started crimefighting. Who designed her suit to look similar to Batman's? Who suggested to her that she wear a Bat-symbol at all? Jacob did. Why didn't he suggest that she join the Colony from the very beginning? Easy: it's a top-secret black project, not something he can just discuss with anyone. Plus, he wanted to get her used to acting as a Bat-vigilante while he completed everything with them, and possibly so he could use his rank to perform a bit of nepotism. The events of Elegy derailed his plans again due to a rift forming between him and Kate. Also consider that during the last fourteen issues of Batwoman's solo series, Jacob is nowhere to be seen, and Kate even mentions at one point that she hasn't heard from him in weeks. What's he off doing? Working with the Colony.
Using Wally West as the POV character. Wally represents everything that DC tried to get rid of with the New 52. He's a legacy character using the same hero identity as his mentor. He was married and a father. He genuinely loves being a superhero and has fun with it. He's also the first of the original Teen Titans to take up his mentor's code name and by far held it the longest. He's also the one who never had any major conflict with his mentor.
It isn't the first time Superman was divided into red and blue energies of himself, so "pre-Flashpoint" Superman being the original Superman's Blue energy and New 52 being the original Superman's Red energy makes complete sense. It makes even more sense following the actual Red Oni, Blue Oni trope! It also explains why Lois and Lana became red and blue versions of Superwoman.
Where are Wally's children, Jai and Iris? They were with him when he was last seen in Convergence: Speed Force. Since then Wally has somehow been lost in the Speed Force (although how he got there after the events of Convergence: Speed Force isn't explained). Are they stuck in the Speed Force? Have they ceased to exist? Has Wally forgotten about them?
I'd guess that it's actually this world's Wally West, since he was established to have been lost whilst with the Teen Titans, with his memories of how things are 'supposed to be' given by the Speedforce. So they wouldn't be with him since they haven't been born yet.
The "fabric" (for lack of a better word) of the DCU hasn't been completely restored, and there are tons of "who is who" questions stewing. If Wally remains Kid Flash, they'll come down the line.
Same with Roy's daughter, Lian. He just got her back in Convergence: The Titans, only to have her taken away from him again.
Dr. Manhattan's involvement in the New 52 may initially seem like Character Derailment, since Watchmen ended with him becoming an optimist, but remember what caused him to become an optimist: his ex-girlfriend Laurie had a father who once tried to rape her mother. Given Manhattan's loose grip on humanity, he probably came to the conclusion that moments of tragedy could give birth to things of beauty. Of course, The Darkseid War proved that wasn't the case, as the child of two consenting villains wound up becoming another Darkseid.