I would make the Riddler the primary villain of the third film, and have the Joker essentially make a cameo by being on a video-feed from a padded room at Arkham, straight-jacketed, his hair a total mess and just flailing about so you can tell its the Joker, but can't see his face clearly, and you just hear his laughter.
In terms of REFERRING to the Joker, sure, just not on-screen that much: but referring to the events of TDK, sure, why wouldn't they?
My idea is that the Joker's speech about "people don't care about if things go "according to plan", even if the plan is horrifying" is presaging the Riddler just as Gordon presaged the Joker with his escalation speech at the end of BB.
The idea is, the Joker is Batman's antithesis: he represents utter Chaos and Batman represents Order.
But the other great Batman villains take aspects of Batman that make him good, and take it to an extreme that is evil. For example, the dualism they show with Harvey/Twoface, who in the Nolanverse is a vengeful vigilante like Batman, just taking it to the point of murder.
The Riddler represents "Order" taken to a crazed extreme; the Joker wants to destroy civilized order; why would the Riddler do that? Would would understand his riddles if all the libraries burned? No. The Riddler is going to be the reaction to the Joker, just as the Joker was the reaction to Batman.
The Riddler wants Order, his own intricate Order, at any cost. He doesn't care who gets hurt, it's all a game to him. That's the difference; Batman actually cares about people.
Furthermore, as that "Psychology of Batman" special pointed out, he's basically got Narcissistic Personalithy Disorder, like Ted Bundy: a driving need for *attention*, to the point of taunting the police and leaving self-incriminating clues to his crimes.
with the Joker, it wasn't about money, it was about a driving need to destroy all established order (be it the police or even the relative order of the mobsters)
with the Riddler, it's about a driving need for attention, and intricate order
***I envision it as some "Enemy of the State" type thing where the GPD sets up a London-esque CCTV system all over the city, high-tech control of the whole thing....****again, presaged by how Batman destroyed the super-sonar device after he uses it for the extraordinary circumstance of the Joker.
The Riddler is either going to make something similar to that, or the police are and then the Riddler will just hack their computers, and he'll basically turn all of Gotham into his giant video game. Redirecting traffic lights, fooling rival gangs into going to the same bar than killing each other when they meet, hunting Batman with CCTV, etc. (I compare to Enemy of the State, but its also a similar idea to awful recent movie "Eagle Eye")
but the thing is the Riddler just wants attention; and the contrast is that Batman doesn't want praise for what he does, to the point that he would voluntarily take the blame for what Twoface did rather than let Gotham get demoralized.
The ending would be something like the Riddler (on streaming live webcast) is confronted by Batman and the Riddler figures out that Batman couldn't have killed those people and that Harvey did, but that Batman was willing to take the blame. Batman is afraid that everyone will be really demoralized and Gotham will fall apart, but instead, everyone gets so moved that Batman would sacrifice his reputation for Gotham that they find their new hero in Batman.
***Further, Nolan was directly asked "wow, they say Twoface killed 5 people but we don't see him kill that many" (Wuertz, Malloni's driver, probably Malloni, and possibly counting Harvey himself....actually probably not because Gordon wouldn't have included that in the kill count)
but there's one or two people unaccounted for; Nolan acknolwedge this, and said the unrevealed people killed would be a plot point in the third film. Riddler loses someone close to him, then goes nuts? Ultimate Revenge of the Nerds?
