I don't think Megas inherently had those issues by nature so much as active choice. Whereas the future super mechanics are inherently such by nature and tend to skew towards a "rich-get-richer" problem by inherent design, Megas are fine overall, and I don't even dislike them in terms of execution because they did a good job at buffing many Pokemon overall. Even several popular ones who got them still needed them because power creep was getting to them by that point (*ahem* Charizard). I didn't mind Salamence and Metagross getting Megas because the latter was rapidly losing viability starting in Gen 5 and nowadays has fallen off dramatically in competitive anyway, and pseudos getting Megas isn't inherently a bad thing because competitive proves stats aren't everything as not all of them are actually prominent in competitive or remain as such, seeing as how Tyranitar and now Garchomp have started falling off, while the only ones who are doing well at present are Baxcalibur, Dragapult, and Dragonite.
In that sense I would disagree that Megas inherently were style-over-substance, because they have more depth to them and actually put effort into improving the Pokemon who got them individually, even if some could be argued as not necessarily needing them per se.
A real example of style-over-substance in terms of super mechanics is signature Z-Moves and Gigantamax forms, which inherently compete with a more generic version of the mechanic and are in 99% of cases entirely flavor driven with no substance to differentiate them from the generic version of it battle wise: G-Max Forms are entirely differentiated by a different G-Max Move that is literally "same as the generic Max Move but we swapped out the original base effect for a new side effect". Signature Z-Moves were in most cases entirely flavor as well with a few exceptions, those being Kommo-o's Z-Move (omniboost effect that ultimately translated to a new generic signature move for Kommo-o in later games), Mew (can summon Psychic Terrain so that's something of value), and Eevee (stat omniboost even if it doesn't help much).
With that said I do have a few things to address regarding your other points
Not sticking to three-staged Pokémon. Mega Evolution pretty much single-handedly killed what rest of hope regarding traditional cross-gen evolutions, especially since you can still use one Mega Evolution at a time. Gen 4 overdid the cross-evos, but several Pokémon still benefitted it even today, while Mega Evolution implies that cross-gen evos shouldn’t even be a thing anymore as second-stage Pokémon and even single-stage Pokémon receive one regardless of BST.
While it’s obvious that a Pokémon getting both a Mega and a regular evo in the same generation would be ridiculous, it does mean that getting a Mega Evolution have left the low BST two-stage and single-stage Pokémon poorly futureproofed. If Mega Evolution were exclusive to three-stage Pokémon and those two-stage or one-stage with pretty high BST (~490 BST is a reasonable threshold), then Mega Evolution will be more consistent regarding which Pokémon could reasonably receive one without going into a complete gamble.
I think this really depends on your personal preference and perception, but I genuinely doubt Game Freak actually cares about the fact that Megas would hypothetically kill the idea of the mons who received them getting a traditional evolution, because I think they probably wouldn't give those Pokemon traditional evolutions anyway, as much as some fans may not like the idea. Game Freak likes to incorporate personality and their own creative visions into changing Pokemon they've created beforehand, and for every Pokemon that did get a Mega, they felt that a Mega was the ideal step forward to furthering their design in those cases, and that was that.
I don't think it's a matter of "cross-gen evos shouldn't be a thing anymore" considering they went back to them several generations later as we now have things like Annihilape and Kingambit, and the latter incidentally would fall into the category of "didn't really need an evolution per se, but Game Freak had a cool idea of how to further Bisharp's evolutionary line and felt that an evolution in Kingambit was the way to do so creatively speaking", which proves Game Freak
Mega Evolution was simply the approach they wanted to do back when they started doing it, and a "super-transformation that is lore-wise a temporary evolution" that they assigned the mons that did was in their eyes the way they wanted to add onto the lines they did give it to.
Two-stage and single stage Pokemon getting them may seem like a loss to us fans, but to Game Freak that mattered little to them because they felt that a super form was the ideal way to add to them instead of a traditional evolution for their own creative and personal reasons most likely. Sableye and Mawile will probably never get traditional evolutions yes, but I don't think Game Freak would have any intention of giving them one anyway: to them the two likely felt complete as is and a super form was the ideal "upgrade" for them combat wise.
I think while Game Freak does sort of try to keep a sense of competitive balance (mind you, they care about VGC more), they also like the sense of not every Pokémon being created equal. While Megas are absent from the games, I've said it before but I also sorta consider it an extension of Dexit which we all know at this point is clearly a final decision for the games.
We're a battle oriented forum with people who play Pokemon mainly for the battling aspect so obviously opinions on different battle mechanics will differ because to us, a Pokemon's battling capability in competitive is what we care about most, but Game Freak generally likes the concept of flavor. They like worldbuilding in terms of creating Pokemon, and Pokemon is still fundamentally at its core an RPG, with an RPG design in terms of its monsters and the world they live in.
"We always have this base criteria at Game Freak of being able to explain why a certain Pokemon is in the world or why it exists in that world, trying to make it feel believable within the fantasy." - Junichi Masuda
And in general, not everybody is necessarily into Pokemon for competitive/hardcore battling, so while a vocal minority has varying opinions on super mechanics, ultimately lore and what Game Freak feels is most appropriate for a Pokemon's in-universe lore and flavor is what matters to them most when they do things like regional forms, new evolutions, or Megas.
Which is to say, Pokemon who got Megas would never have gotten a traditional evolution to begin with, because Game Freak likely never felt a traditional evolution was the logical way to add something to those Pokemon from a worldbuilding point of view.
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Treated as a “fix-all” even if it really isn’t. Not all cross-generational evolutions and regional forms improves upon the original. While Mega Evolution was intended to give a boost of popularity to Pokémon thay receive one, only very few managed to stay strong popularity-wise, as there are not a lot of fans who like the Mega Evolution and also liked the original. Execution matters more than you think, so this means that while losing an unappealing Mega Evolutuon is a blessing in disguise compared to being stuck with an unappealing cross-gen or regional form, it is also a complete waste of Mega Stone. Speaking of which..
Pokemon is a *big* franchise with a big fanbase, so naturally there are so many different opinions on things. I've said it before in another thread but whenever you add to something that already exists, not everyone who liked the original is going to like the new addition. It's not exclusive to Megas itself. It's happened with traditional new evolutions and regional forms alike.
Mega Stones and the “Item Bloat”. Item bloat is quite inevitable, especially today due to “filler evolution items”, but the Mega Stone also run similar issue since they have to be held by the Pokémon just to make them work. At least Z-Crystals are compatible to any Pokémon thay have a compatible move of matching type (exclusives are mixed bags), while Mega Stones have only one purpose which, while there are good reasons, also means you’ll end up having to collect 20, or even 40 of those stones, even the Mega Evolutions that you hate if you are a completionist. Doesn’t help that most of them are “find them in a shop / hidden in the ground”.
The only way I can think of a “fix” to combat further Item bloat is a G-Max Factor inspiration that make it so Pokémon with “Mega DNA” from their ancestors can Mega Evolve with a Key Stone; not all Pokémon have this potential. The Mega DNA can be removed or given through a Mega Stone, which is now “unspecific”. I won’t tell more to avoid wishlisting.
Item bloat is probably something that's a pain in terms of coding as time goes on but it's most certainly not an issue in individual games especially since most mainline games from Gen 4 onwards offer unlimited bag space. Game Freak generally likes flavor and specific items to them gives a nice sense of worldbuilding.
Mega Stones have always been part of Mega Evolution's flavor and they probably wouldn't change that. The G-Max Factor parallel idea is also not exactly great especially since Dynamax was specific to Galar and we now know that having G-Max Factor on an individual specimen creates transfer lockout in HOME because those individuals cannot leave SwSh without having it removed (which you need the DLC to do so, another mess). Tera Types were easier to deal with on the other hand, which may create implications for Terastal in the future (namely being just as generic).
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I rambled quite a lot but had a handful to say. Ultimately I think it's also important to remember that while this is Smogon and thus our opinions are leaned into competitive battle performance, Mega Evolution was in many ways a mix of flavor and substance that worked.
They simply didn't bother to do it afterwards because they had other ideas they wanted to try in later generations, and like with cross-gen evolutions, which stopped for a long time after Gen 4 before being done again with PLA and SV, they can always return to them if they feel they have new ideas for it from a worldbuilding standpoint (which mind you, is one of the more important priorities to them). Megas are something with their own individual traits that incorporate worldbuilding and gameplay.
We're seeing Game Freak's constant shift in creative philosophy even right now: Regional forms were common in Alola, Galar, and Hisui, but SV has dialed back on them a lot, giving them to only two Pokemon, while they tried out convergent species (unrelated new Pokemon who are incredibly similar to their derivative counterparts) and the Paradox Pokemon, which probably aren't going to be expanded on past Gen 9.
). The part-Grass ones would have enjoyed an EQ resistance and Tentacruel/Gengar would have much preferred to not be weak to Psychic/EQ.
