I like the thought put into this. I really agree the Black Mask angle; especially after watching the Under The Red Hood animated movie they put out recently. Black Mask could make a great villain who's "realistic" enough for the Nolan Batman movies.
I'm strongly against the Clayface idea, though. I get what you're saying, playing up the "man of a thousand faces" angle and make his "shape shifting" more of a disguise thing, but you know how fans will react to that. Don't ruin Clayface; as much as you think it could work, deep down, you know it wouldn't. Not that drastic a change to the character, anyway. He needs his powers to be the great villain that he is.
Same with Penguin; I wouldn't go a whole movie with a Penguin villain and avoid calling him that save for like a minion or two saying it and Hardy getting pissed (assuming he was Penguin). He just needs to be an eccentric, dirty-dealing businessman that could maybe connect the underworld and business world secretly or something.
Also, I think you may have forgotten about Talia. You mentioned that Nolan used Rha's Al Ghoul, but you know he had a daughter; a daughter than actually had a son with Bruce Wayne in the comics at one point. She could make an appearance in this movie and maybe be part of a Catwoman, Batman, Talia Al Ghoul love triangle?
Chances are this 32rd (and final I believe) movie will have more than one villain; perhaps two major ones. I wouldn't be surprised at all if it were something like Black Mask, Riddler, and Catwoman.
For each of the past movies, there has been a mob boss (Rupert Thorne for the 1st, Falcone for the 2nd). Black Mask would be the Mob leader for the 3rd movie while Riddler is the more "known" villain (like Scarecrow/Rhas Al ghoul were for the first and Joker/Two-Face for the 2nd).
Have them work together and maybe Batman works with Catwoman (she walks between good/evil throughout the film, ultimately helping him in the end). Who knows? It could work out great. Hopefully it won;t be too much longer until we actually hear something concrete regarding the villains for the 3rd movie.