Personally I just think they should just bring Two-Face back. I think Eckhart had a lot more potential in him and falling off a ledge just wasn't epic confrontationish enough for me. Also, his return would clear Bruce's name and totally just ruin everything he and Gordon fought for.
I know they were originally planning on bringing The Joker back for the third one in a supporting manner. Gary Oldman thinks that they should recast because it's what Heath Ledger would have wanted. And I agree. Using The Joker only once, despite being Batman's archenemy, seems kind of limiting. But who they would get to replace him? Well, I have no idea. The only question is who would have the balls to want to follow an iconic performance like that.
The Riddler sucks. He's a comedy character. He's almost a parody of The Joker. He's one of those guys who never really made the transition from Adam West to Frank Miller very well. But if anyone could make him work it would be Depp.
I like the idea of The Penguin. But only as a supporting character. Like The Scarecrow. He's just not in The Joker's or Two-Face's league.
In The Batman Universe there are 4 main "Big Bads": The Joker, Ra's Al Ghul, Two-Face, and Bane. I've always liked Bane, even though he looks like a Mexican Luche Libre Pro-Wrestler. He scared the crap out of me when I was a kid. Being a calm, cool, calculating, intellectual gentlemen one minute then transforming into a bloodthirsty, hulking, savage, brute the next.
Think also they should put Catwoman in there as the girl Bruce eventually settles down with. I'm a big Bruce/Selina shipper, so I'm biased. I thought Rachel was a useless, uncharismatic waste of screen time and didn't care one bit when she, well you know. As a main bad guy, a professional cat-thief doesn't work for me. As a supporting character/love interest, then yeah that works for me. I heard Angelina Jolie really wanted the part. Which is a given because she plays "the sexy, hot chick" in every single movie. And even then half the time she's sleepwalking through it. So, yes, I find her acting very limited and tiresome. I throw her in the same league as Halle Berry and J-Lo. They're Media Figures, not actors. I like Eliza Dushku myself, but someone suggested Rosario Dawson which would be good too.
Then someone suggested an idea that I liked. In the wake of The Joker's reign of terror, a whole new generation of costumed criminals have popped up, thus escalating the situation even more. Poison Ivy, The Riddler, The Scarecrow, The Mad Hatter, Killer Croc, etc. Either Two-Face or Ra's Al Ghul returns to lead them on a crusade of chaos and terror to take back Gotham for the freaks and criminals . To make matters even worse , either Harvey or Ra's is armed with the knowledge of Bruce being Batman. That would be good or it could be a clusterfuck.