The gang simply didn't work hard enough! They're getting old and too pig rich to stay ahead. You can see how laid back they all are when you watch the behind the scenes video.
When they made Raiders there was so much more pressure - which made Spielberg more inventive, so much more focussed and working on overdrive. He learnt his lesson from 1941. It was as if they were fighting a war when they made that film. Now its a very casual matter of, "look what we can do on the computer now" and "I promised Kate I'd be home for dinner, so its a wrap everyone".
Also, sometimes when a script isn't working, its best to toss it and do something completely different. This is an example of not doing that.