The problem with comparing Megas to Regional Forms, is that they are mechanically very different from each other. Mega Evolution is a temporary power boost, and out of battle, the Pokemon is in its original form, so it definitely feels like the original Pokemon more than the new form. Regional Variants also have a lot more differences than Megas in terms of designs and mechanics.
For starters, Megas are a temporary transformation, so the design can't be too drastic of a change. If you look at Mega Venusaur, you'll notice that it has a larger flower and some vines, Charizard-Y is pointier, Kangaskhan's only difference is that its Baby comes out, and Gardevoir's dress gets bigger. There's not much room for a drastic change because its temporary.
There's also a limitation on what can be changed for a Mega. For Megas, only stats, (excluding HP ) typing, and Abilities can be changed that will have a noticeable impact. Things like move pools, secondary abilities, evolutionary relatives, and the HP stat are things that can be tampered with Regional Variants.
For example, look at Alolan Ninetales VS Kantonian Ninetales. They look extremely different from another, and have different, stat spreads, abilities, and moves. Their roles don't overlap at all, Kantonian Ninetales for example, uses either a Nasty Plot or Choice Specs set to be an all out attacker, while Alolan Ninetales is pure support with Aurora Veil. As a result things like check and counters vary as a result, with Garchomp being an hard answer to Kantonian Ninetales, while not being an answer at all to Alolan Ninetales. Things like teammates would also vary: Vensaur would take advantage of Drought, while Shell Smash Blastoise would take advantage of Aurora Veil.
In contrast, both Salamence, Gyarados, and Tyranitar could do Dragon Dance sets with or without their Megas, and things like teammates and counters would stay the same. They would benefit from dual screen setters, and both would need teammates to cover Ice, Electric, and Fighting types respectively, with or without Megas.
Anyway, the point I'm trying to make is that Regional Variations have more mechanical variation than Megas to the point that they can be be seen as completely different Pokemon. I've always disliked calling Regional Variants the same Pokemon- they mechanically function like separate Pokemon.
Late reply time again!
Either way, I don't really agree with you about everything.
Megas and regional variants are completely different from each other in terms of the actual mechanic, I agree about that.
But I disagree about regional variants being more different in terms of design and general mechanics though. First, regarding designs. I think there are a lot of regional variants that look too similar to the orginal form, which is one of my issues with (some) regional variants. The most notable being several Alolan forms such as Geodude, Graveler, Diglett, Rattata and Raticate. From the Galarian forms, the two most notable so far are Slowpoke and Yamask. And even so, I think most other regional variants are still very similar to the original form to the point that you can still tell what Pokémon it is supposed to be. Take Ninetales, for instance. The main difference between original and Alolan Ninetales is the color. Alolan Ninetales also has a little more fluff (or what you should call it) on its fur. Other than that, they are both Nine-tailed foxes. Personally, I think the only regonal variant to be different from the original form to the point that I would have thought it was a new Pokémon rather than a regional variant if the game hadn't told me what it is first is Galarian Meowth. While some parts of it clearly resemble original Meowth, the overall design is way too different.
That said, I think many Megas look far too similar to the base forms as well. The most notable are Pidgeot and the Kanto starters (minus MCX). I remember when I first saw the Kanto starter Megas getting revealed, I thought they looked too similar to their base forms. Looking through all Megas now, I don't think there's any Mega that looks like it could be a completely different Pokémon in the same way as Galarian Meowth. But I guess that's a good thing, Megas and regional variants both need to have resemblance to the original Pokémon.
Regarding stat spreads, that is another one of the issues I have with most regional variants so far. In almost all cases, their stat spreads are too similar or exactly the same as the original form. Taking Ninetales as the example once more, the only difference in terms of base stats is that Alolan Ninetales shifts 9 points from Attack to Speed compared to regular. Now I don't feel like going through every single regional variant, but I think the one that did stat shifts on a bigger level is Galarian Slowbro which has a bit more Attack than Defenses compared to regular Slowbro. Overall, I think regional variants have a lot more potential to be different in terms of stats if Game Freak decides to go even further with them in the future. Which there's a chance for since they continued with regional variants in Gen 8 after all, and we haven't seen everything from Galarian forms yet!
In comparison, I think Megas generally do a better job in terms of stat distributions. Sure, some are just plain upgrades over the originals like Salamence and Metagross, but others go from zero to hero. Lopunny and Mawile for instance, their Megas are just plain better than their base forms. And some do just complete swaps like Pidgeot which goes from an epitome of mediocrity to a decent Special Attacker.
That said, I suppose regional variants can still function very differently from their base forms even if they have the same or almost the same stats. But in Ninetales's case, it seems to be more because of its typing and Ability rather than the stat changes. And regarding Abilities, the two forms of Ninetales do just have two different weather-starting Abilities as their HAs, so they aren't that different on that front either. Though I personally think that is a very cool thing, some regional variants have Abilities that are just variations of the Ability that the original form has.
So I don't really agree that regional variants are a lot more different than regional variants in terms of mechanics and performances.
I also want to say that I really like Alolan Ninetales, it is actually one of my top 5 favorite Alolan forms.
Regarding Megas being used very little during the main story in X/Y, I always got the impression that they wanted to make Megas feel more "special" in X/Y. Only a small number of trainers are capable of using it (the player, the main rival, Korrina, Lysandre and Diantha - five in total), there is some heavy lore surrounding it and how not everyone can master it. It was also possible to only find Mega Stones during a certain hour of the day during the post-game. But it seems like they more or less dropped this whole idea after X/Y since Megas got a lot more prominent in OR/AS. The same goes for Gen 7 where you can buy Mega Stones at the Battle Tree shops, and a lot of opposing trainers at the Battle Tree can use Megas as well (since some Battle Tree sets are just Mega sets). Perhaps an unpopular opinion of mine is that I actually liked the approach X/Y had to Megas and how they managed to make them feel special in a quite good way by making them a bit elusive. But I understand that many others don't like this approach, and I guess that might be the reason why they changed things in the games after X/Y. Though I'm okay with the post-X/Y approach to Megas as well. It also makes me curious about how Megas would have been handled in "Z" if that had been a thing.
Lastly, I want to say that I do not consider either Megas or regional variants to be "new Pokémon". Both of them are just different forms to me. Neither have separate Pokédex numbers, so they are not new Pokémon by strict definition. Regional evolutions on the other hand, those are new Pokémon in every way since they do have new Pokédex numbers.
And lastly, while were on the topic of Pokedexes, I think the DP are the most generous games when it comes to version exclusives. Between DP themselves,
only 48 were missing out of the 493 Pokemon, all of which were either starters or Legendary Pokemon with the exception of Tangela and Tropius. So despite a questionable regional dex, DP are arguably the best games to complete the National Dex, or at least within the initial paired versions.
This is actually a very good point, and something D/P doesn't get enough praise for. The same goes for Gen 4 in general since Platinum and HG/SS also included a vast majority of all Pokémon that existed at the time. Sure, some of them require inconvenient/tricky methods to get, such as GBA insertion for the Sinnoh games or the Pokéwalker and the horrible Safari Zone for HG/SS, but even so, there's no denying that they wanted to include as many Pokémon in all games. And it is possible to get every single non-mythical Pokémon between all Gen 4 games.
In comparison, let's take a look at how the other generations did in terms of including all Pokémon that existed at their respective time:
Gen 1: Had all existing Pokémon by default
Gen 2: Had almost all, only missing Gen 1 starters, legendaries and fossils
Gen 3: Had several Pokémon missing from each individual game installment, but it was possible to get all Pokémon across R/S, FR/LG and Emerald
Gen 5: Also had most Pokémon but not all, and some had to be obtained through various annoying means like White Forest, Hidden Grottoes or Dream World, the latter which no longer exists
Gen 6: Same as Gen 3, though X/Y on their own featured a lot of Pokémon, almost 600 I think? Not sure though, and still less than D/P in terms of percentages
Gen 7: S/M had less than half of all existing Pokémon, while US/UM have considerably more but far from all,
Gen 8: Dexit. That said, they will still have at least 2/3 of all existing Pokémon once the Crown Tundra is out. And I guess even after that, the generation isn't over yet
So I think Gen 4 did very well when it comes to including as many Pokémon as possible in the games. It was by far the best in terms of including as many Pokémon as possible (in terms of percentages) in each individual game installment.