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By expanding on this, I think some of the entries used were already around since the XY or ORAS days on the Mega Evolution's pages on their websites.
It wasn't a big deal back then, so it makes no sense for it to mean they hate them.
Yeah, that's correct. But those got less attention because far fewer people read the websites than play the games.
(Unfortunately, they eventually took those sites down before I had a chance to preserve the information. I have a text file on my computer where I've been saving all the little species bios and things from the official websites, starting from Sun & Moon. I've even tried Wayback Machine-ing it, which might be able to work for the XY stuff, but won't for ORAS due to the way the site was designed.)
Ultimately, I think those entries are just meant to show that Mega Evolution infuses the Pokémon with a huge, barely-controllable amount of power. Many of them just extrapolate on details that already existed for those Pokémon, like Scizor overheating in battle. That's been a part of its profile for a long time, and the Mega Evolution entry just amps it up.
Building on that, I think the implication, such as there is one, is that this is why it's crucial to have a strong bond with the Pokémon that's Mega Evolving. That aspect of the lore was completely disregarded by the core games' mechanics, but the anime and Super Mystery Dungeon both showed that Mega Evolution can cause a Pokémon to run berserk, and in the anime in particular, it's the bond between the Trainer and their Pokémon which stabilizes the transformation. (Everyone else might've hated it, but I still think it would have been cool to tie Mega Evolution in with Affection.)
At any rate, I think saying that those Dex entries display a "regret" on the part of the developers is like saying Black & White's story shows they "regret" coming up with Pokémon battling. Just because the narrative is critical of its own elements or willing to highlight flaws in them doesn't mean the developers want to cast these things off completely. Even Dynamax received some internal criticism in its debut game, via Piers and the state of Spikemuth. Plus it almost destroyed Galar!