Yeah, I'm pretty sure there are huge chunks of the story missing. But then, Akira is such a huge story that it took up several huge graphic novels. I'm quite sure they cut out a lot of content to keep it from going on too long.
It's still a pretty good anime, though, all in all.
Yeah, the ending was a little on the stupid side but it made sense the way they explained it. Tetsuo, Akira, and the kids all had power beyond humanity so it made sense that with all that power they would create a new universe since they were gods.
Odd side note: As soon as I saw the part where Tetsuo turned into that giant organic mess I remembered the episode of South Park with the trapper keeper.