I just saw the documentary, and I was turned off when Jodorowsky spoke of how he wanted the movie to show the effects of LSD on the audience. I have no patience for surrealistic films, and I definitely have no patience for hallucinogens, so the rest of the DVD was a chore.
I also don't accept their contention that this proposed film influenced all other films - I can accept its influence on Alien and Blade Runner, because the teams from Jodorowsky's proposed project went on to work on these films, but I don't accept it impacting Star Wars. As any copyright lawyer can tell you, there are similar themes all through literature, but that does not mean there's any influence, because most themes are variations on each other.
My proposed project would be more, shall we say, simple - it's asking, what if there were a series of technological changes? This is the central question of science fiction, and I would deal with the impact on civilization as well as on individuals. No surrealism, no magic mushrooms, just some speculation to that question.