If you understand how his kit works, you'll know he'll never be "Useless".
He'll be relevant for most likely a long time- even if Ninjas come that specifically counter him just due to how overloaded his kit is.

Ninjas that counter "Specific" ninjas, never completely stop something that's being used because they over price the crap out of it so only a small portion of the player base ever gets their hands on it- Susano Kakashi is a good example of a Ninja that has the potential to counter him but if you purchase it, then you're purchasing something that isn't necessarily "strong", just something that counters certain line-ups in which case it's a terrible purchase for someone that doesn't have the resource to * on it, so an even smaller portion of the community has it because you might as well spend that resource on Shisui or the next powerful ninja AGK, Minato, etc.

There's also no draft system when fighting other players, so you choose "Best possible scenario" set-ups.

For him to faze out, something must come along that's out right better & just as easy to obtain, which will eventually lead to you complaining about that next broken thing :)