I dunno, it's just that I got a feeling that some Legendaries are pushing it further. Then again, it is just me. I wish I know VGC better.I feel bad telling you you're wrong for 2 posts you've made in a row, but VGC doesn't work like this. The roster of Pokémon that are allowed rotates each year, and each generation tends to go regional dex without legendaries -> national dex without legendaries -> national dex with legendaries. This is done specifically because of the issues you identified, where players who don't like the higher power level of Pokémon like Zacian or Xerneas can just sit out the one year they're permitted, or at least they've had 2 more years with a more normal power balance. Changing the meta each year also prevents it from getting stale.
I don't think legendary Pokémon being overpowered is a bad thing. It'd be a little ridiculous seeing Celebi getting easily knocked out by a Vileplume when the former is supposed to protect inferior creatures like the latter. Mewtwo was genetically engineered to be a super-weapon, so it'd be strange if it were weaker than Alakazam. Yveltal is supposed to be the harbinger of death, so it'd be odd seeing it get walled by a Porygon2. It's part of the worldbuilding that they're too strong, and serves gameplay by allowing the lategame to be difficult because if a kid gets really frustrated by the game's difficulty they can just use the region's legendary and autowin.
I think balance in this game is poor because of the complete other side of the coin. There are Pokémon out there lacking even a theoretical niche. Having a Wigglytuff or Stantler on your team will always put you at a disadvantage against a standard team because their stats are simply too low, so they should be boosted a bit.
Mega Evolutions is another story, though. I do like the concept but it's the execution that leave much to be desired. Most of them are not supposed to be as powerful as the likes of boxart Legendaries (+600 BST for most, maybe, but then you can't hold an item), and yet focusing on popular Pokémon getting it proved to harm the concept more than it gives good for the franchise in the long run. At least less popular Pokémon are getting it in ORAS, but by then the damage is done.
While there are definitely some who does benefit it, with Kangaskhan, Lucario, Mawile, Sableye, Medicham and Lopunny (and to a honest to Arceus extent Charizard) benefiting their own Mega the most, there are those who don't really needs it (even for just design upgrade), such as Gengar, Alakazam, all of the Pseudo-Legends (though it don't have too big of an impact on Tyranitar and Garchomp), Blaziken (though this is balanced by the other Hoenn starters getting one as they do needs one to an extent), Gyarados, Scizor, the Lati@s, and Charizard having two (though it do comes with a bonus of unpredictability). I'm not mentioning the boxart Legends since, as Celever said, they are supposed to be powerful.
One will say an excuse that the popular ones do need a "design update". Unfortunately, I personally think that even as separate forms, the Regional Variants did the design update better than Mega Evolution does, as I feel a good amount of the Mega Evolutions feels really unnatural and not in the right way. Some others are unnatural but at the time, still fitting to the species. Plus not everything really needs a design update; Gengar is simple but effective, and I'm glad that it's Mega (as obscenely overpowered or at least obnoxious to deal with) did managed to update its design in cohesive way. Others kinda overdid it in design, even Mega Swampert (it was funny at first sight, but it does feels a bit awkward in retrospect).
And what's worse is that I also found Regional Variants way easier and fun to make than Mega Evolutions (not that I don't have any fun of making my own Megas of course, but I never participated in Megas for All unfortunately). And not all that difficult to balance unless you are dealing with something with low BST (which is solved by Regional Evolution unless you have something already at third stage, and even then, you can at least give them an unique niche). The only true blunder in term of becoming overpowered is Galarian Darmanitan, and that's mostly because of Gorilla Tactics proving more useful in practice than on paper.
tl;dr Mega Evolution is good concept, questionable execution at best, with given to mostly popular or already great Pokémon not helping the situation. I prefer Regional Variants in the long run because it updates old Pokémon in more natural ways and less stressful to make it balanced.