So...currently watching XYZ anime endgame and it made me wonder something- you've pointed out Ash's Greninja being the one in Ultimate. So, do you Ash would've felt anything from this? (if not it's probably the same reason Rex most likely doesn't feel the same pain from Pyra/Mythra getting hurt if it's not for their post game life) Better question: do the Hands realize it's a pokemon from the anime-verse?
I've actually been trying to figure that out since I got to that part of the anime. I'm inclined to say no? Mainly because the way the bond phenomenon works in the mainline games is different from how it works in the anime, plus the whole "different universes" thing. In the mainline games it only activates once it KOs an opponent (though the flavor text says that it "became fully charged due to the bond with its trainer"). The fact that its appearance is still based on Ash's suggests that it's still tied to him though (tho in SV it doesn't transform at all). Though if we're talking Ultimate specifically, it could easily be done the same way that Lucario, Mewtwo, & Charizard can mega evolve without a trainer bond or even a mega stone (again, leaving Ash unaffected).
The Hands absolutely would realize that it was from the anime that's like the big reason why they invited it. Smash is filled with pokeani references--hell you could put it to a debate whether the Pokemon rep in Smash leans more anime or games. The Pokemon Stadium/2 stages are 100% inspired by the anime gyms and are not a games thing (despite what their names might suggest). All that to say that even if they didn't realize it right away (that is, they met Greninja before finding out) they'd be quick to identify it.
That does remind me of a random half-baked theory I thought of a bit ago: the letter Sun (the protagonist) receives in his mailbox at the start of the SM demo could be from Smash post-Ultimate.
Seemingly knows a Lot about Sun including his name, that he'd be moving into that specific house, and the fact that he was moving in from outside of Alola, all before he or his mom even arrived, gifts a Pokemon of a specific variant only previously seen in a separate continuity, total lack of a name or sender address or any identifying information, no one mentions the letter again after this point... yeah I think you can guess why I came up with this one.
Of course, if that is the case then that begs the question of "how did they get Greninja into Smash in the first place". To which the answer is either time paradox or that they have access to the animeverse, neither solution I'm real huge on.
