While thinking about it some more, I realize that for as much as I love the two most recent films, they're still not the kind of Batman movies that I would make. For me, I would make something that's a little closer to the Animated Series, just with higher production values, obviously. That series (the one that ran in the '90s - not to be confused with The Batman - which is a decent cartoon, but not as iconic as the previous incarnation). That show managed to make Batman himself a realistic (I'm using that term very loosely here) character, and even his world was believable despite the fact that they'd incorporate elements of science fiction and fantasy.
With the current series of movies, they've established a world that's as realistic as this sort of a thing can possibly be. While I have no problem with it, and I definitely prefer it to the "anything goes" mentality of the earlier films, I realize that this probably leaves out a lot of villains and characters from the Batman mythology that simply wouldn't work in this current series.
So, with that in mind, I'm focusing on characters that I think are great, but I just don't think that they'd work well in the next movie.
Mr. Freeze - Just like how you should forget about Halle Berry as Catwoman, you should forget about The Governor of California as Mr. Freeze. I'm not talking about that guy - whatever the hell he was all about. Actually, Freeze was a pretty lame villain in the comics even - a "second-rate Captain Cold" as the Joker once said. It wasn't until the Animated Series came along that he became one of Batman's best, and most tragic, foes.
Dr. Victor Fries had his sick wife cryogenically frozen while he searched for a cure for her ailment. Thanks to the crooked boss who ran the company that worked for, he got into a horrible accident, leaving him unable to survive in anything warmer than sub-zero temperatures (hence the suit). Seeking revenge, he was willing to break the law in order to get satisfaction.
That's some classic comic book supervillain stuff there. Unfortunately, it just wouldn't work against Christian Bale's Batman. It's just wayyyyy too sci-fi. You'd have to change him so much that he'd be unrecognizable.
Poison Ivy - Forget about Uma, okay? She certainly looked good, but that's where the goodness ended. The problem with Pamela Isley is the same as Mr. Freeze. Her origin story involves a similar theme of corrupt businessmen and a freak accident.
It's a pity though, because she's a classic femme fatale/temptress figure. Much like how Catwoman could fulfill both a villain and love interest role, there are a lot of possibilities with her. I suppose it's possible to do something with her in the current series, but again so much would have to be changed. While a "fear toxin" seemed to work in Batman Begins, I'm not so sure that her kiss, which turns men into her mindless slaves, would work as well.
Clayface - He's a really cool visual, but I'm not going to get into his origin story. (It's wayyy too damn convoluted - but the Animated Series managed to simplify it.) But the problem is that you have a big shapeshifting guy. If they ever manage to create a new series where they inject some fantasy and sci-fi back into the mythology, then he'd be a cool one. I'd leave him out of the next one though.