I dunno if this is spoilers, cuz it's just my interpretation, but eh. Better safe than sorry.
[sblock=spoilers?]The 'main' plot is speculative fiction about how humankind might evolve in the future. The whole 'Akira' project is designed to accelerate human evolution. That's what Kei's trying to say when she's babbling (in the English dub at least) about amoeba and energy and so on.
But she makes the point that if you artificially evolved an amoeba at a vastly accelerated rate, so that it becomes something as large and as powerful as, say, a person, it still wouldn't BE a person. It'd be an amoeba, with all the power of a person.
This then is an analogy to what the scientists did to Akira...and then to Tetsuo. They figured out a way to kickstart their evolution into a much greater being...but for all their super-powers, they're still just human kids, with all the baggage that entails. Tetsuo's massive inferiority complex and towering resentment of the other kids sets loose his abilities in the most destructive of ways. By the end of the movie, he's gained a bit more perspective...but in the end, his mind simply isn't powerful enough to contain the energies that were infused into him. The process that was begun in him cannot be stopped...and he continues to evolve wildly, out of control.
Then Akira shows up. He'd undergone the same basic process, and at the end of it he managed to complete his evolutionary journey by becoming a creature of pure psychic energy; free to explore the infinite cosmos. Of course, in the process of converting to energy, so much power was released that it looked like a nuclear weapon had detonated. This was misinterpreted (by human beings) as a pre-emptive strike, and led to another world war...that ends shortly before the movie has begun. Akira returns when the three "old kids" the other test subjects, send out a psychic call. He then guides Tetsuo to achieve the same transformation...resulting in yet another cataclysmic release of energy.
It's basically a movie that explores the very dark side of the human psyche, then asks, "What happens if you give a human being...this craven, treacherous creature...all the power of a god?" Well, it's a disaster.

Of course, there are other, more positive viewpoints of humanity tucked in there too, but on the whole it's a pretty pessimistic and dark narrative.[/sblock]