I guess to wrap this up like Nolan wanted to do he had to circle back to League of Shadows. The LOS was never referenced in TDK which for me makes returning them a bit meh. It'll be like circling back to the Ten Rings when no mention was made in IM2, despite the implication they were there. Would it have been so tough to toss out a LOS reference in TDK?
This was an issue for me as well. Aside from the bits with evil Harvey Dent, TDK may as well have not happened. TDKR was far more a direct sequel to Batman Begins; I feel like the whole Joker story may as well have not happened. While it is arguably the best of the series, TDK doesn't really fit in with the other two movies.