You can try to justify it by out-of-universe-prespective reasons as much as you want, by my example proves all E4 members are not equal. Some E4 members like Flint are exceptionally strong, while some E4 members like Aaron and Lucian aren't that strong.
I'll admit the out-of-universe thing wasn't the best reason, but that doesn't change the fact that those were still two completely different battles in two completely different circumstances. Cynthia could have had a different strategy, or maybe Flint was just better prepared. That doesn't automatically mean that Flint is better though.
Also, it's worth mentioning, I just went back and rewatched the Cynthia vs. Lucian battle, and there's actually no reason to believe that the battle is just beginning at the point we come in. It easily could have already been raging.
My point is that the fact that Diantha was feeling the pressure and Mega Evolved Gardevoir suggests that even is its Water-veil form, Ash-Greninja posed a significant threat to Base Gardevoir, and so in full-form, it can definitely take on Base Gardevoir at least. And Diantha is a Champion, so her Gardevoir without Mega Evolution will be obviously stronger than E4 Aces. And if you look clearly, Diantha wasn't completely holding back in the last Shadow Ball- it was a huge one which was overpowered by Water Shuriken.
And my point is that just because she Mega Evolved, doesn't mean she automatically started using her full power. Since she started the battle going easy, it stands to reason that when she stepped things up, she didn't do it all the way, only just enough to test Greninja's strength. I'm not denying that Greninja could take on normal Gardevoir, but that's not the point here. As for that Shadow Ball, you have no way of knowing if that was supposed to be full power or not.
Look, you're overestimating the E4 too much. Remember that E4 non-aces are not as powerful as E4 aces. Do you really think that Cynthia's Gastrodon and Glaceon are as powerful as her Garchomp? Champion's and Elite Four rely mostly on their aces, there is no way that their non-aces are as powerful as their aces. If Ash-Greninja takes out the ace of an E4, the rest of GPCISS can take on the E4 non-aces.
Well, I say you're underestimating Elite Four too much. Maybe their non-aces aren't as powerful as their aces, but that doesn't mean they're pushovers either. Given how skilled and powerful the Elite Four are, it wouldn't make sense for them to have one Pokémon that completely outclasses their other five. Their aces are the one's we see them use the most, that's why they're their aces, but that doesn't mean that they get that much less training, or are that much worse battlers.
I don't think so. I believe Diantha and Steven's aces are as powerful as the aces of the other Champions and when they Mega Evolve then their aces are in a different level than the other Champions. It's reasonable to think that there is a parity between all regional Champions, and so, without Mega Evolution, all of their aces are equal.
I agree that there is parity between Champions, and that parity is measured by the power of the Mega, not the base. Think about it this way. A trainer goes through their journey and they follow a "power curve," that is a path moving from weaker to stronger. Diantha and Gardevoir would have had a small jump on this path because of Mega Evolution. Because of this, Diantha would have reached Champion-level power sooner than a trainer not using Mega Evolution. Her Mega Gardevoir would be at the power of a Champion ace, but that doesn't mean her normal Gardevoir would be, because she would have used Mega Gardevoir in any serious battle. I'm not saying Mega Evolution is crutch, I'm simply pointing out that there's not really any reason for Diantha's Gardevoir to be as powerful as Cynthia's Garchomp without Mega Evolution.
Plus, Diantha's Gardevoir has demonstrated that it's incredibly powerful without Mega Evolution. Gardevoir destroyed Magnus's Absol without Mega Evolving, and Magnus was the previous Kalos League Champion. Whereas, remember that even Torterra even managed to land a damage inducing hit on Bertha's Hippowdon. And Gardevoir was also effortlessly besting Pikachu without Mega Evolution. Yeah, so there is conclusive evidence that Diantha's Gardevoir is above E4 aces even without Mega Evolution.
I'm not saying that Gardevoir is weak without Mega Evolution, I'm just saying it may not be on the same level you're putting it on. Magnus may be a powerful trainer, but he did nothing to prove he was on Elite Four level. As for besting Pikachu, you must remember that Pikachu's strength fluctuates wildly. Pikachu was far from its strongest when it battled Gardevoir.