1) The Akira Project was an attempt to create superhuman children to propel Japan's economic miracle and make the country the world's #1 superpower, which I took as a metaphor for the Japan school system and its emphasis on cram schools and kids following a specific academic/school choice/career track for success. Kids who don't follow that track are deemed losers. Which is where many future manga and anime artists found themselves.
2) In the film, Japan's suppression of the Akira Project was meant as a metaphor for Japan's failure to come to grips with its own militaristic, violent past, i.e. its behavior in WWII. The re-emergence of the Akira Project, in the form of a violently transformed Tetsuo, is a sign of Japan's suppressed, violent past coming back to haunt it.
At least those are my interpretations based on multiple viewings of the film. Whether all that is in the manga or not is immaterial to me. Every film needs to be judged on its own.