If you want to accept the premise that Ash-Greninja isn't E4 level, you have to accept that
1) Malva threw the match, which has zero evidence to back it up
I personally support that theory and there's no evidence to back it was legitimate either.
But that aside Malva's not really relevant to whether Ash-Greninja is E4 or not. Ash-Greninja never fought any of Malva's Pokémon. Simply because Alain's Charizard could beat Mega Houndoom doesn't mean Greninja could. Greninja lost to Charizard every time they battles and the leauge wasn't really close.
Even if I conceded the battle was legitimate and that Charizard X is indeed an E4 level Pokémon, that fact that Greninja failed to beat it three times with no prospect of that changing puts Greninja far below it's league. If Greninja had acutally beaten Charizard it would be a different story. All Malva's battle proves is that Alain can beat both her and Ash. I
Back to my real world example. A world class Tennis player could beat both another world class player and a school player, but that wouldn't put the other world class player and the school player on the same level. All it would show is that the first is capable of beating the other two.
2) Diantha mega evolved her Gardevoir for no reason, since if AG is below E4, he would be quite far below champion level. Unless Diantha is incapable of judging how strong her opponent is, there is no need to mega evolve (even Paul's Torterra was a complete joke compared to champion aces)
Mega evolving doesn't mean she believed it was necessary to defeat the opponent. She was probably just testing Greninja's strenght.
Diantha did not loose that battle. Landing a single hit, even if it seemed significant, doesn't put Greninja in the same league. Not when Ash lost to a regular gym-leader a few episodes later.
3) Alain saying that battling with AG "takes me to new heights" after beating Malva is not clear enough to be considered evidence, even though it sounds pretty obvious. I can't think of anything else it can mean.
Given "takes me to new heights" is a vacuous statement that doesn't really mean anything, it can't be used as evidence that Greninja is E4 level. Alain enjoyed the battle and complimented Ash for it - as has every trainer he's faced in every league. It's nothing more than a compliment. Ash has never actually beaten Alain despite battling three times and there's no reason to believe he actually could.
Not only that, plus there is clear evidence in XY&Z25 that Diantha was pressurized to Mega Evolve Gardevoir due to Base Gardevoir struggling against Ash-Greninja. And even after Mega Evolving, Ash-Greninja momentarily overpoweed Megs Gardevoir sending it flying back yelling in pain, significantly gaining the upper hand, which E4 aces like Flint's Infernape were unable to do against Cynthia's Garchomp.
Ash-Greninja getting one hit on Mega Gardeviour and Flint's Infernape not getting a hit on Garchomp aren't really comparable. They're two differnet sets of trainers under two very different sets of circumstances. What's to say Cynthia isn't a better trainer than Diantha.
I think you're overestimating the significance of Greninja sending Gardeviour flying back. It's not obvious that it was significant at all - earlier in the battle Gardeviour had sent Greninja into a tree and Greninja got up and continued to battle. Unless Greninja can acutally be said to have definitively won, there's no reason to assume it was capable of doing so.
Raichu Focus Blast also got sliced through by a Dragon Claw took Raichu out in a single hit. Focus Blast is a Fighting type move and Dragon Claw is a neutral move offensively against Electric types. Mega Sceptile's power was clearly evident.
And still made it to Top 8 of the League.
The dominance is surprising though. Infernape having a massive type-advantage over Aggron and Ninjask didn't show that dominance.
I don't deny that Mega Sceptile was on a different level to Raichu or that it was powerful. I'm denying Sceptile is E4 level.
Tierno making the top 8 isn't that impressive - That's only one rung higher than Ash got in the Indigo league and Kalos has significantly fewer participants - only 64 in total. Indigo had 256.
Yes Sawyer's Pokémon dominated Tierno's. But all that show is that Sawyer is a novice or maybe intermediate trainer who's better than another novice. That doesn't put either of them near the E4 level.
And it's not fair to compare Sceptile's battle to Infernape's from DP. Again that's an entirely different battle involving two differnet trainers and two different sets of Pokémon. Paul and Ash were more or less equally matched and using Pokémon with relatively the same strenght and ability. Sawyer was using his strongest Pokémon, with boost of Mega Evolution against a marginally weaker trainer.
Ash-Greninja went toe to toe with Mega Gardevoir for about 7-8 minutes, equally matching Mega Gardevoir's attacks, repeatedly pushing Mega Gardevoir back and ultimately sending Mega Gardevoir flying back overpowering it making it yell in pain. No Pokemon in the show has pushed a Champion's Pokemon that hard, not even E4 aces. It's an E4 level worthy feat without doubt. No one is saying that Ash-Greninja beat Mega Gardevoir, if it did so, it'd be Champion level. But since it pushed it so hard, it's E4 level without doubt, no E4 level Pokemon has gone that far against a Champion's Pokemon.
Ash-Greninja landing one hit on Mega Gardeviour is not an E4 worthy feat. An E4 worthy feat is winning the battle or coming close to doing so. And we haven't really seen any full E4 vs champion battles so there isn't really a fair point of comparison. And that assumes Diantha wasn't just testing Ash-Greninja in the first place.
Are you seriously suggesting that Paul Chimchar landing a Fire Spin on Cynthia's Garchomp which did basically nothing is comparable to Ash-Greninja bulldozing through Mega Gardevoir's Shadow Ball and sending it flying back in pain knocking it down onto the ground?
Yes. The animation in BW and XY is noticeably more dramatic than pervious series. A lot more Pokémon are sent flying into things when they hadn't been before. Greninja had been thrown into a tree earlier in that battle, but still got up and continued to fight. Gardeviour got up and looked as if it were able to continue to fight so it's significant shouldn't be overplayed.
Diantha was surprised by the strenght of Greninja's attack, but that doesn't mean she couldn't have turned the battle around. Being able to keep pace with a champion Pokémon doens't make Greninja an E4 level Pokémon. Only a decisive win could do that.