I'd read somewhere also that a problem with the group of people in Crystal Skull is that they were all superfluous. Seeing him constantly bailing out the others in Last Crusade is what actually cemented their purpose in the storyline. You keep reinforcing how much of a badass he is, having to save people from tanks, and draw gunfire, and everything else. In Skull, they were trying to justify Marion's presence, and cement Shia as being the heir-apparent to the adventure legacy, taking off the focus from Indy time and time again.
It would have worked better if they just stuck to the Last Crusade formula of having him get sidetracked to bail out the others a few times, and keeping the action focus on him. Even though Connery, Elliott, and Davies were all getting in the way and mucking things about in Crusade, I never once considered them useless characters, because they served to keep the spotlight on Indy.