"Raiders" had one of the best macguffins in movie history. It was friggin' perfect and used brilliantly in the film.
"Raiders" is one of the best movies in movie history. It's a masterpiece, everything perfectly in place and nothing unnecessary.
You can have a good movie without a great macguffin. Even a very good movie, in the case of "Temple of Doom", which is a helluva lot of fun, but, of course, falls short of the one-of-a-kind greatness of "Raiders."
The stones were vague, they were obscure...unlike the foreboding conversations about the Ark with Indy, Marcus and the government agents in "Raiders", all we ever learn is that they're "rocks with magical properties" and that they can glow and get hot. Nothing terribly interesting or intriguing about them, but the rest of the movie (with a few flaws notwithstanding) was very entertaining.
At no point did we REALLY believe that Mola Ram and his weird cult were going to somehow use the rocks to destroy other gods and take over the world! On the other hand, putting the Ark into the hands of the Nazis is a pretty frightening concept.
The Holy Grail was a better goal, more name recognition and at least we were told in the beginning the reasons why the Grail is important and why someone would want to possess it. It was perfectly serviceable for the movie, was somewhat awe-inspiring in spots, but again not quite at the level of the mysterious and intimidating Ark.
The Crystal Skull....well, the movie's flaws were so myriad and so huge that talking the problems with the macguffin are almost insignificant compared to the other issues. But, yeah, the skull was again a little too esoteric and vague, though I think it could have been used to better effect in a better screenplay.
Ultimately, I think the macguffin DOES matter, but not as much as so many other elements.
You can certainly have a very fine, very entertaining movie with an average (not bad) macguffin. But for true, inspired greatness, you need to have everything in place, as only the original "Raiders" did.