One of the highlights of this new series is seeing how the old villains are re-imagined, or trying to figure out how they'll be done if they haven't shown up yet. I wouldn't want to see these movies do away with that.
I would argue that nothing terribly radical has been done with most of the villains. Joker was simply translated straight from Killing Joke and Arkham Asylum - if anything it was enjoyable to finally see him come to screen as he is in the best comic stories. Scarecrow was barely even in Begins, and there were more tantalizing hints to his character in that movie than any real development or new interpretations. The closest thing to real change was in merging Ra's and Ducard, and taking away the supernatural elements of the character, which, granted, was a vast improvement. I honestly couldn't care less about seeing further familiar villains show up as I don't think that including them in any way automatically improves the quality of the stories. If anything it threatens them as the creative team has to try to shoehorn them in, instead of having the freedom to go where the story leads.