I get the feeling that there was just so much more story to tell and feel like there is probably a really awesome 3.5 hour cut and they just went through and haphazardly chopped out portions that weren't as important.

Don't get me wrong, I really enjoyed the film, I just think there were things that should've been developed more. The edits were just so jarring at points and it didn't feel like a Nolan film. I don't think I noticed it as much in the theater because it was the true IMAX "wow that looks awesome" experience.