IMO Made of win!
I remember reading Harlan Ellison's rehash of David Lynch version of Dune's pre-production woes in Watching, and hyperbole doesn't do it justice. I think the biggest problems producing any SF extravaganza are artistic focus and $$$.
Jodorowsky's El Topo showed he had vision and a sense of humor in spades.
Whether he could make something as epic as the Dune series through the fourteen hours of a miniseries IDK.
I've heard of him getting HR Giger to do art direction and several other insanely tasty possibilities, but getting backers with the $$$ and patience to let him pull it off was IRL the biggest challenge.
One alternative is Jodorowsky films a documentary a la Terry Gilliam's Man of La Mancha about how cursed his production of Dune was!
Edit: Well, thanks to your wiki links, Frank Pavich actually did a doc on it! My bad!
I'd love to have seen AJ's vision pulled off. Splendid mess hardly even scratches the surface of how wonderful it could be! Supposedly Frank Herbert really dug AJ's version of it but considered David Lynch's version an abomination.
I thought Lynch's film kind of blah. Too truncated and you can blame a lot of reasons why it didn't quite come off.