Seeing as this is Bruce Wayne's rookie season as Batman, I thought the escalation theme of TDK would take an even more aggressive turn coming into further sequels. In BB, the gates of Arkham Asylum were forcibly opened and chaos ran amok in Gotham City by Ra's Al Ghul, so I don't see why some other criminal mastermind (i.e, Bane) wouldn't try it once again just to piss Batsy off..
My idea of a Knightfall adaptation is that it closely resembles the comic book plotline, however no Robin or Nightwing would exist, and would fit in nicely with Batman's beginnings as a crime fighter, considering that after 3 movies directed by Nolan, another three-part arc would seem appropriate. A Jean Paul Valley would be ok with me, yet there should be an entire separate movie that would introduce him into the mix and further develop his characterization, which leads into the Knightfall movie adaptation. It could be possible that Jean Paul Valley was actually a student of Ra's Al Ghul prior to Bruce Wayne, only that he was taking the law into his own hands in some other part of the globe. Upon hearing of Ghul's death, he ventures into Gotham City to seek vengeance and there he meets Bruce Wayne. As Batman, Bruce defeats Jean Paul, and confines him into Arkham Asylum. It would also help that Jean Paul actually knows who Batman is, yet due to his learnings from other continents, perhaps somewhere like Japan, he decides not to reveal Batman's secret identity as some sort of code of honor.
Bane enters into the mix upon the next movie, with the same introduction as Joker, without any knowledge of who he is, and upon arriving he breaks out all the inmates from Arkham to once again cause trouble for Batsy and the GCPD. Following the plot of the comic book, Batman grows weary with each encounter of an arch-nemesis.
Prior to Bane's true reveal to Batsy, our hero would have a final encounter with the Joker in the streets at dawn. After defeating and neutralizing Mr. J, Bane introduces himself and gives Bats a hard time, seeing as he has grown physically tired and too weak to give Bane a good fight. Then Bane breaks his back.
In the third and final chapter of the film, Jean Paul Valley discovers Batman has been broken. He decides to take our hero back to the Batcave, and helps him recuperate (with the mindset that only he should bring down the Caped Crusader). As Bruce regains his health, Jean Paul forcibly takes the mantle of the Bat as his own and battles Bane. (I foresee this taking place in the middle of the entire flick, somewhere around the 45minute to 1 hour mark)
Gotham is thankful to this new Batman, yet perhaps after a few weeks they are rather surprised by the tactics he employs upon capturing what's left of the Arkham inmates, namely morally incomprehensible acts of violence by killing off criminals here and there. Bruce becomes 100% and there he decides to take down Jean Paul for a final showdown and an end to the whole plot.
Tell me what you think, all this I just typed on to go so pardon me for any hints of repetitiveness with my grammar and such... (plus, its 8:10am in here and I haven't slept a wink lol)