The Darabont draft is materially better. Lots of outrageous stuff on it, but it's actually got a pulse. The big issue with Crystal Skull in my view is the weird inertness.
I tend to think that the actual story elements of the fourth movie are pretty strong. Lucas basically took some hoax legends about "Akakor" and the Mitchell-Hedges crystal skull and combined them with El Dorado. While I'm sure some would regard the employment of New Age myths as off-brand compared to biblical or Arthurian legend, I think the ingredients were there for a solid 50s-era Indy movie.
The problem is that story is to a large degree storytelling, and Crystal Skull fails to execute on its ideas with any sense of mystery, grandeur, intrigue, or stakes -- all pretty fundamental qualities of a good Indy movie, I would say. It doesn't feel particularly cohesive, either. For example, working in the Nazca lines is a great idea on paper, but they are just tossed in as an image and no attempt is made to relate them to the story in any meaningful way. A lot of the movie is like that, like they shot an outline as though it were a script.
I also think the movie suffers from a lack of decent transitions, which adds to that nettlesome episodic feeling. The way Indy and Mutt go from the sanitarium to the graveyard via a dissolve to a CGI helicopter shot is a missed opportunity -- why not a small amount of Peruvian location footage showing them traveling there, to give us a sense of location? Why go straight from the skirmish with the cemetery warriors (who aren't given even token characterization and are instead just chirping ninjas who serve no greater purpose) to the characters already inside a crypt? Why go from the characters spotting the waterfall to already being in the cave behind it?
None of these things are problems on an individual basis, but in aggregate they cause the movie to feel as though it is just jumping from sound stage to sound stage...because that is exactly what it's doing. Even the subterranean Temple of Doom makes effective use of the location footage it does have, like the Sri Lanka vistas during the elephant trek, or the famous rope bridge climax. I realize these movies aren't characterized by gritty verisimilitude, but Crystal Skull looks like it was shot in a damn hard drive. There is nothing grubby or tactile about it.
I am not suggesting they should have shared tonalities, but you look at something like Apocalypto where the director actually made use of his passport to shoot in Mesoamerica because that's where the damn story takes place, and the contrast in the believability of its visuals says it all. And that's despite a movie that has a rather "video" look due to the cameras used. Spielberg shot Indy on film but seemingly did everything in his power to ensure it wouldn't look that way.