I see what you are saying, but I disagree.
This is Joker we are talking about, his story is never done as long as Batman's story isn't done.
I look at TDK as an introduction to the Joker, it just wouldn't make any sense to leave out Batmans ultimate nemesis in the finale to a epic Batman trilogy. There needs to be some closure, some absolution on their relationship.
And as I've said before, I don't think Joker would be the kind of guy to sit in his jail cell twiddling his thumbs whilst the guy who "completes him" is running around getting hunted down by cops and other villains. Just doesn't make sense to leave him out IMO.
I wouldn't have him as the main villain though, but you don't need to have Joker as the main villain. He could be a literal jack-in-the-box, popping up randomly to cause chaos for both the good guys and the bad guys.