For Batman 3, I could kind of see it going this way- it's obviously open for changes, as it's kind of a rough idea... I would edit this a lot more to make everything tie together much more cleanly if I were to ever completely write it out:
The few remaining mobsters left from the mobs from The Dark Knight are trying to rebuild their alliances and power that they lost due to The Joker's path of destruction and Batman's interference. They rebuild their banks, businesses, crime rings, etc., and slowly begin to regain their lost hold on Gotham's underworld.
However, The Joker's men seem to have united again- clown masks and all- to try to steal from the mobs yet again- only this time, the robberies are happening much more quickly... First, the businesses, then the banks, then attacks on the crime rings themselves. However, instead of death threats, clues are being left as to just who is stealing from them... This time, it turns out that it's not The Joker, but instead, The Riddler.
The Riddler/Edward Nashton: Drop the Nygma, as I just don't see it fitting the character in this series... Seems to '60s Batman for me. A narcissistic sociopath who believes himself to be the "better class of criminal." So narcissistic, that while he's aware that he's committing crimes, he sees his actions as a form of Justice- and here are where the parallels to Batman can begin to be drawn (much as Joker tried to compare himself to Batman in TDK). Both are trying to take down crime in unethical ways. Batman may even go so far as to start becoming discouraged yet again from crime fighting.
However, someone on the inside of Riddler's operations is stealing from him: enter Catwoman:
Catwoman/Selina Kyle: A cat burglar working for The Riddler as her means of getting money, with plans to break off on her own eventually. However, she is not only stealing for her own good, she claims to be looking for something more (which would turn out to be traces of family links within the Falcone family's mafia- hinting at the When In Rome storyline). Throughout the film, she becomes more and more distraught with not having any family or loved ones to turn to, while at the same time, refuses to let anyone into her personal life (giving her that cocky, hard-to-get personality she has in the comics)... Namingly Bruce Wayne.
The story behind Bruce and Selina/Batman and Catwoman could pan out to the old phrase, "Is it better to have loved and lost, or to have never loved at all?" Basically, Bruce doesn't understand Selina's tendencies to avoid his closeness- which she does because of a horrible childhood, in which she had no true family nor any true love.
On the other hand, Bruce finds out about Rachel's plan to marry Harvey, which drives him to anger, which in turn puts Batman into an even worse public eye than he was before (after being blamed for the murders Two-Face committed). Bruce tries to move on to Selina (perhaps with anger toward Rachel in mind, treating the situation almost as if Rachel were alive and would physically notice if Bruce and Selina were together). It would come around to Bruce admitting his feelings toward Rachel to Selina, where Selina would lash out at Bruce for having had the ability to love and be loved before, and that he should have cherished Rachel for what she was (much like family) rather than being angry at her for wanting a happy life.
-Back to the crime aspect- The mob needs help to combat the robberies and the attacks at their power, so they seek to hire a mastermind to help combat The Riddler, Batman, and Catwoman. Here's where the next "freak" would come in:
Here, I could go one of three ways: Bane, Mr. Freeze, or Black Mask. My choice would be Freeze. Here's my interpretation:
Mr. Freeze/Victor Fries:A very despressed scientist who hangs on the edge of sanity due to what's happened to his wife, Nora, who has fallen terminally ill. He has put her in a cryogenic stasis to keep her alive while he finds the cure for her disease (sound familiar?), and sees that the mob can help him get the means to do so, under a few stipulations, however. He will only provide his resources to get the money back- he will not harm, maim, or kill others (particularly because he's living the experience of losing a loved on, and does not wish that on others). As for his armor, the best way I could see it happening is that he has locked himself in a cooled suit that keeps him cold constantly, as "punishment" for and a "reminder" of what his wife is going through (keep in mind, he's not thinking straight, and is blaming himself for his wife falling ill, much as many spouses would if his/her wife/husband were dying). As for the gun, I don't know much about science, but I could see it being a gun that pours liquid nitrogen, which freezes his targets on contact (not to a point that would kill living beings, only enough to make it very hard and uncomfortable for them to move).
The mob sees Freeze won't go the full nine yards against Batman as they would want him to (and see him as the only apparently capable person of doing so), so they set up a situation in which Batman and Freeze would be drawn to Nora's location, in which Nora would be killed and Freeze would believe Batman to be responsible (yet, as any loved one would and as I previously stated Freeze did, he finds himself responsible for, again, not being able to save Nora). Here is where the overall theme of the movie comes in, redemption.
Batman wants redemption for Gotham, Harvey, and maybe most of all, Rachel (when he realizes that his head is in the wrong place about her). The mob wants redemption for themselves, and seeks a regain in power. Selina wants to redeem herself for whatever reason it was that "her family didn't love her enough." Freeze wants redemption for Nora's death, by killing Batman- while destroying every bit of Gotham if that's what it takes to get his hands on Batman.
