From the outside it looks like a superb deal, but issues are in the details. Most notably, the Museum is being proposed on PUBLIC land and thus the conflict in meeting the requirements.
As quoted in the article from Presidio Trust board member:
“If it’s your land, you can do pretty much what you want,” Bechtle says. “But with public land, there is just a higher level of scrutiny.”
The trust developed design guidelines for the site. The building could be no higher than 45 feet; as for looks, the trust didn’t want a building that replicated an old-fashioned architectural style...
...in short Lucas proposal didn't meet the guidelines and he didn't want to compromise.
Personally, I think the museum is a fantastic deal and any city would be blessed with the gift -- still hoping SF & Lucas find a mutual agreement (one of which not be exclusive to Lucas items/curation).