If anything, it's really Snyder's and Goyer's ability to handle these two characters that worries people that most since the two had issues handling just one of them in MOS.
I'm oddly not worried about Batman. Just avoid the Miller extremes (in particular the AllStar ones, and parts of TDKR), and have Batman as a non-deadly detective/strategist who knows good martial arts. Since his athleticism is a given (Gym Jones and whatnot) and Zack tends to have good martial arts/street fighting (Rorshach vs the police is how Batman should fight) I'm not too worried. Also, the costume will probably be really good.
Since the number one criticism of Bale's Batman tends to be his voice/smartness, I think they might OVERCOMPENSATE by having Batman be one step ahead of everyone. If they can avoid doing that, I'd be fine with it.
Now, Goyer must avoid retreading his own Batman. That'd be hard to do.
Also, the Bruce Wayne aspect doesn't have to be in there much. There are a lot of stories where Batman is just in the suit.
As for casting. I'm not worried at all. NOT at all.
Snyder doesn't care about star power. He wants someone who can command the screen.
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Now for Superman. I'm worried. I'm worried that they won't be able to BUILD from MOS, that it will feel like a stand-alone more than a true sequel, that a true sequel may not happen, that Superman will come across as dumb, weak, or both to prop up Batman.
Also the time committed to both might create a narrative that feels like a shared movie, when Clark NEEDS to have a movie mostly to himself in order to develop as a character in a focused manner.
Also they should be friends near the end, or at least ALLIES. No VS stuff for the longterm, and no Batman beating Superman.
Every effort to make Superman look cool will have gone to waste if that happens.