JOvan said it right: they found it too earlyu, we found out way to early what the deal was and in the end, you shouldn't reallye xplain too much wehat it really is... The trick about a McGuffin is to lose it somewhere during the ride.
The Ark, a whole lot of stuff going on, but we only find out if it's real or not in the end... and then we get sand... and it gets locked up as a mystery. We still don't really know what it is or what makes it tick. It comes down to saying summin' like real great power doesn't succumb to greed.
Same with the Sankara stones: Indy seems to get it but only on an existential level: doing good makes life better.
The Grail: fair enough: poor cup, gives eternal life but with enormous limitations. In the end it's not about the Grail but about the leap from the lion's head: faith.
The Crystal Skull: we get the lot explained to us. And from very early on. There's not much left to discover for the rest of the movie, and then at the end... we get the rest. THey forget to ditch the McGuffin. Hitchcock would turn in his grave.