Yuffie only takes up to a certain number of materia. It is generally enough to wipe someone out who has not put in a substantial amount of time leveling and buying extra materia, but it is only a capped amount. I have gotten beyond it before, and been left with some materia.

Additionally, I think I am the only person in the world who both likes Yuffie and the Wutai sidequest. It can be challenging, sure, but it's fairly deep and entertaining.