Mat Block should be able to stop the Beast Ball, since it works pretty much the same as Protect except it fails to stop status effects from attacks, which luckily it seems Beast Ball doesn't have anything like that, so it should be an effective block. Double Team, Smokescreen and Substitute should distract Isobu long enough to give it an opportunity to attack, and Role Play should allow Greninja to copy Isobu's Mist's illusions. Spikes should prevent Isobu from being able to move too much, and it has versatility in terms of its close-range attacks, like Cut and Aerial Ace, and its long-range attacks, like Wayer Shuriken or Hydro Pump. (I have got to make a CRT for Greninja. He is missing a lot of moves on his profile.)
Now, granted, the fact that Isobu has an extremely strong shell that would be hard to penetrate, and if Greninja gets swallowed by Isobu, he'd have to deal with all of the miniature Isobu's within his stomach, I think that Greninja has a fair chance of defeating Isobu, considering he's scales to the power of other Mega-Evolved Pokémon, which have been shown to be able to take on certain Legendary Pokémon. Plus, this Ash-Greninja has Ash with him, and the help of his Trainer increases his chances of success all the more. I'm gonna give it to the frog with mid to high difficulty.
Winner: Greninja
