If I had to choose, I would go with Pearce over Depp. I think that if they did go with Depp it would overshadow Christian Bale, like Ledger's Joker did last time. I don't want the Nolan movies repeating the mistake of the previous Batfilms, of making the villains more interesting than the hero. Batman became interchangeable and the focus was on how eccentric they could make the villains and the big names they got to pick them.
Pearce is well regarded, can play an effective villain, but wouldn't overshadow Bale. The focus of the Batfilm should be on Batman. Also, I think Nolan missed a good opportunity by not making Anthony M. Hall the Riddler in The Dark Knight. I thought he would've been a good one.