I don't understand if you could show me one person who enjoyed and payed attention to the game that would say the Crystals aren't important to the game I would be shocked. You have to relize that many people disliked FFIX and then make things up about it why it is bad (many being people who only liked FFVII and/or FFVIII).
For example they'll say things like:
"The story made little sense and sucked!" Now of course us fans of the game know that is not true.
Also you'll here....
"The game wasn't futurisitc which made it bad!" Now immediately after that you know that you are dealing with a fanboy/girl of FFVII and/or FFVIII, the two most futuristic games in the series.

So to some up what I said, your letting fanboys\girls affect you too much, FFIX is a great game and the story made sense, it was complicated but if you payed attention throughout the game and put the pieces together you cannot say parts didn't belong and made no sense, it was a pretty plothole-free game.