Yuffie didn't steal all of my materia

[Rantz]

I don't think there's an order of preference, I think she takes the first 48 or so starting with what's equipped on the characters and then moves on to the materia stock, starting at the top of the list and then working her way down.

You may be right, I found that info in a random walkthrough. Although I do seem to remember having a few materia still equipped right after the theft.

odd how there is a preference for Leviathan when you can only obtain that summon after the Wutai sidequest.

Square probably plans for people using GameShark and such, or maybe Leviathan was originally meant to be obtianable without Yuffie or something...

Also of note is that any materia you have obtained through GameShark will be taken and will not be returned along with the rest.