Stop is only really a problem if it can be used indefinitely.

Although I hate to credit MMOs with much of anything in terms of game mechanics, most use stuns fairly well (actually, debuffs are used relatively well in general). A single player can't stun things indefinitely, because the ability will be on cooldown or disabled after use, making timing when it is used important. PvP fights also frequently feature an internal resistance to stuns that builds up and makes you more resistant or even immune the more you get hit (which doesn't change the fact that stuns shouldn't even be in PvP, as nothing is more boring than not playing the game).

Similar things could work really well in most RPGs. Make Stop only usable every so often, or give foes a building resistance that keeps it from locking them down completely. It won't really change the way it works against random mobs, but it will make it usable, without being broken, against bosses.