Couple of thoughts really.
He's an interesting choice. Academy Award Winner Ben Affleck is probably unlikely to see a major Hollywood style payday like this ever again, so it's probably the best moment in his career to do something like this. There's a lot of good feeling between Warner Bros and Affleck just now, and not only will Batman vs Superman be a huge payday for him, it also puts him in a franchise which might see him possibly direct a Batman or Justice League film (with a small role for Batman) in the future. So either way, even if he's rubbish he's done a good thing, and if he turns out to be good he'll get a blank cheque from Warner Bros to do whatever the hell he wants. If that leads to more films like Gone Baby Gone, The Town or Argo, then I'm all for this.
On the other hand, we've only just forgiven him for the massive amount of **** he'd done before he started doing his own films, so if this goes pear shaped all of that will be forgotten.
It's probably appropriate to wheel out all the Heath Ledger talk. Many were wondering what Nolan was playing at casting him as The Joker. It worked well, and people who are outraged at those who are outraged for the choice of Affleck seem to be using this argument to demonstrate that we might be in for a surprise. The problem with that argument, though, is that Nolan is a great director who's a half decent writer himself and has a particularly good writer in his brother. The Snyder/Goyer combination contains significantly less talent both on and off screen, so it's not a fair comparison.
Conversely, having Affleck on board is probably good from a creative stand point because we know he is a better writer and director than both Snyder and Goyer, so having him cast his eye over a script and tweak his character accordingly can only be a good thing when we consider just how rubbish Man of Steel is.