Even if Greninja had protean, which as much as I would like to believe, the problem is AT this point it makes no sense to assume it does. Though I wouldn't be surprised if "Ash-Greninja" in the games had Protean.
I just don't think Protean MATTERS until its mentioned in the anime. So we have to assume unless contradicted officially Greninja keeps its dark typing.
I just wanted to point out that this is nearly irrelevant because we don't actually know what the stats/typing/abilities of Ash-Greninja are.
Pretty sure we have to assume Greninja is faster and stronger, while very little was gained in defense BECAUSE of Alain's Charizard's Blast Burn. Which implies it cannot take direct hits.
We also don't know how strong the new Water Shuriken actually is. All we have to go on is that it's stronger than Mega Gardevoir's Shadow Ball which, even without STAB, is pretty strong. You can't automatically make the assumption that Moonblast would then stop Water Shuriken because A > B and C > B does not imply C > A.
But you're forgetting, Moonblast is not only a stronger attack than shadow ball, it also benefits from STAB.
The only plausible way to believe that Water Shuriken would be STRONGER than the CHAMPION'S Ace's STRONGEST move. Is if Ash Greninja had a SEVERE increase in the attack stat. We're talking about a 75 point increase with maybe the remaining 25 point increase in speed if game-wise Ash Greninja is like mega evolution and Greninja gains a 100 stat boost.
And even then the only feasible belief that it could overpower Moonblast would be if it had an ability that increased Stab.
I can give Ash Greninja the benefit of wild unrestrained unlimited power but even so I very much doubt that would be as effective. Shadow ball was used for plot purposes.
I'd definitely be singing a different tune if we had the same thing but with Moonblast, but Shadow ball LITERALLY is pointless move on Gardevoir except for ghost types especially against a Pokemon like Greninja which means it made perfect sense to use, because it was the most believable move that could directly strike Greninja without knocking it out (resistance) and a move that can be overpowered. Since Shadow Ball is not benefited by it unlike say Mega Gengar, in which case the move of choice would likely be dark pulse which is identical to shadow ball but it doesn't benefit from Gengar and is resisted BY Greninja.
If the challenger comes up with something that surprises the Champion enough that she almost loses, then I doubt the referee would call a red flag against the challenger for being 'unfair'. The Champion is supposed to think on their feet and take the appropriate counter measure. Assuming that she was just playing with Ash, the very fact that Diantha let the match tip so badly against her favor means that Ash had done well enough that she couldn't come up with a counter measure.
She was testing Ash, seeing what he would do, she never had time to come up with a countermeasure because this was something she had never seen before. I'm sure even a champion needs time to figure out countermeasures to something never seen before. When you're dealing with completely unfamiliar territory you can't just pull out something out your butt that "might" work in countering something different.
A champion would need time to see the battle, play defensively, FIGURE out the weakness of the opponent Pokemon. Time is what Diantha needed, Time was not given to her. But eventually Diantha would've countered Ash Greninja figuring out its weakness and then using it to her advantage.
After all how many times has Ash done the same thing. Figure out a weakness or exploit a weakened side to acheive victory. He did it in the Olympia Battle and he did it here again BEFORE Ash Greninja which allowed Greninja to strike Gardevoir, it was a very similar tactic Ash used against Olympia and her Meowstic.
And for an example but I'm going to be vague, because it's the point that matters then the actual example and this is from a different show.
There was a Character (A) who was Fighting Character (B). B had an ability that was hard to counter and seemed unfair. A needed time to counter it. Taking hits and blows from B using his ability, A figured out how to counter B and therefore was able to fight on a more even playing field.
It doesn't make this impressive showing worth any less for Ash.
I never said it was, I was saying not to overpower Ash and Greninja while sacrificing what Diantha represents. Ash can get clean hits on a Champion's Pokemon without thinking that Ash could've knocked out Mega Gardevoir as well, and only didn't because of a convenient "Ash falls unconscious"
