Time Stop isn't broken, it's a ****ing 9th level spell. Casters who can use 9th level spells are the same kind of people who would chew up and spit out Superman. And heck, even he turned out to be able to make time stop (and reverse).
At the time they're able to cast 9th level spells, things like Time Stop should be already be in common use by their enemies, in addition to things like Celerity, Foresight, & Contingency. And any villain without at least two backup plans involving Stilled Silenced Greater Teleport and liberal usage of minions isn't well enough prepared to deal with near-epic level characters.