I agree that there were sections of the movie that I had a hard time trying to figure out where it was headed. But I chalked those up to the standard issues of other "origin" movies where the director has to introduce the main characters, explain what makes them tick, bring them together, work out their differences, and resolve everything with rainbows and unicorns, all while trying to fit a plot in there, too. I expect the sequel to be much more straightforward because we won't have to go through all that again. (See: "Captain America 2")
That said, I thoroughly enjoyed it, and will likely see it again, if only to catch more dialogue and in 3D.
(While I'm old enough to have seen the source material for the second stinger reference, I never did. That didn't stop me from shouting "You gotta be kidding me", though.
)