For chameleon, for instance, combine making the ability to get 100% so hard to accomplish in the first place that only the most powerful (and thus inherently unbalancing) characters can get it with ways for the game to deal with it that make it less unbalancing. If chameleon was hard to accomplish in the first place and 100% was that much more hard to accomplish AND if NPCs reacted to a suspicion that something was there by casting detect life or dispel (or even just by feeling around blindly or taking swings at empty space in the hope of hitting something), that would go quite a ways toward balancing it.