I guess it is just like what happend with the Star Wars prequels. Anticipation and expectation were so high, that, in a way, the prequels just didn't stand a chance.
Then again, it was the fans themselves who made the trouble, because it didn't match what THEY felt the films should be, instead of just going to enjoy a movie.
I think the new Indy film should be OK. The prequels had a lot of background story to cover and somehow match it into what Lucas had already made. This new Indy film is a sequel, a further adventure of, and other than making some nods to the previous films, they don't have to make everything connect, just to tell a good story.
But, I guess any succesful franchise runs this risk when it comes right down to it.