"Prey" was published back in 1991 so it's been 19 years since I read it. I vaguely remembered the story besides remembering I liked it back then and thought it was good. My memory was either a little faulty or my standards have risen since I was 15. (Both.) Either way, I wasn't too impressed with "Prey" overall.
Elements of "Prey" lend themselves nicely to pick up where The Dark Knight left off: the alliance between Batman and Gordon that now has to be kept secret from everyone, Batman being hunted by the police as a vigilante, Batman needing a new Batmobile, and Dr. Hugo Strange becoming the city's expert analrapist on Batman while secretly wishing to be him and replace him.
"Prey" is also more blatantly sexual than I remember, especially for the time. I mean, 1991 was one of the breakthrough years of in-your-face sex in comics, especially in Marvel, where Jim Lee was regularly drawing the X-Men and especially Rogue and Psylocke naked every issue. In "Prey", they go all out with the sex and nudity: Lots of big boobied naked chicks in every issue, Strange has a heavily implied sexual relationship with a Real Doll, he kidnaps the Mayor's daughter and holds her handcuffed in bed in her lingerie. They didn't show Strange raping her but you can presume he did. Then there's Catwoman, who's in the story for no real reason other than as a plot device and to occasionally get naked. That sort of stuff hasn't been in Nolan's repertoire and probably won't make it into Rises.
Ultimately, "Prey" isn't anywhere near as good as I remembered it; it's overly melodramatic, the story falls apart in the second half (it's never clear why Batman didn't immediately suspect Strange and why he didn't monitor Strange's penthouse until the end), and the sub-villain, "the Night-Scourge", who is the cop in command of the Batman Task Force Strange hypnotizes, really sucks. Really, really sucks. He's just a grunt in a ski mask carrying samurai swords.
But in the way, elements of the stories involving Joker, Boss Thorne, and Silver St. Cloud in Batman: Strange Apparitions* (which also starred Hugo Strange) informed Joker, Boss Carl Grissom, and Vicki Vale in Batman (1989), there's stuff here that could definitely - if the rumors are true - be borrowed and vastly improved upon by Christopher Nolan.
*Strange Apparitions is a collection of 1970s Batman stories I do recommend. They're dated, yes, but really high quality stories for the era, and you can see that the wide streets and tall (but not gothic) buildings of the 1970s Gotham City informed Chris Nolan's Chicago-Gotham City. In fact, there are a ton of similarities to Batman in the 1970s and Chris Nolan's Batman movies, including Batman living in Wayne Tower with a Batcave under the city like he had in The Dark Knight.
I have to read Prey before I decide on, but I doubt we will get nudity in a Batman film. We might get the assumed raped as well as someone pretending to be Batman. If you think about it Nolan uses multiple stories for his film. Batman Begins was Year One as well as Tales of the Demon. Dark Knight was Killing Joke and the Loeb/Sale stories. Prey sounds like the set-up to get Strange, a Batman pretender who they can pin Harvey's death on as well as Catwoman. It sounds like the shell of the story, but I expect they are using Prey as the cover and are going to take plot points from other stories. Just stay way from anything Morrison has written about Batman and they will be fine. The sad part of outright admitting to using Prey is you can see the ending from here. They could shock us like they did in the last two films, yet if this is the end, we will see the end of the Burton film of Bruce looking as the Bat-signal is light again.
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Going back to the "upgrading C level villain" part of this, take a look at Fraction's Iron Man, where the Mandarin has raised the power levels of people like the Melter, the Living Laser and Whirlwind.