I thought when they announced the third movie started production Bale had given some early interviews where he either hinted or explicitly stated that this would be his last Batman movie. There were also reports circulating after Ledger's death that Bale didn't really want to do the third one, but was doing it because Nolan was the director. At least partially explains the ending to Nolan's trilogy.

If Batman vs. Superman picked up where Nolan's trilogy had ended, then Joseph Gordon-Levitt would either start to wear the Batman costume or the Robin costume while Bruce Wayne is thought to be dead even though we and Alfred know that he had started a new life with Selina in Paris. Even though it would be interesting to see if Joseph decides to wear the Batman costume (since Bale's Bruce said the costume was a symbol and hinted that it was time for someone else to wear it) or the Robin costume (and potentially go down the Nightwing angle), it would be too much for Batman v. Superman. Plus, I am not sure the writers could come up with a plausible explanation for Bruce changing his mind and return from the grave again especially since Jim Gordon now knows Batman's true identity.