That is a fair point indeed as Let's Go used Megas, but I don't think the Unova comparison is a good one since I would argue they wrote that plot exactly because of trying to make Pokemon battling look good, it's the opposite. I always got that's the reason why Ghetchis' twist exists to begin with, why in the sequels the morality of Team Plasma is reduced to "I stood with N and now understand Pokemon shouldn't be liberated" or "I stood/stand with Ghetchis and am a piece of shit who wants to steal Pokemon". As much as I love the story of these games and N, the main takeaway at the end of the day is "see, despite posioning or making them asleep helping you catch them, you are never forcing Pokemon to be your friends, the one guy who thought that was just being manipulated!" Which, while it obviously fits what most of the franchise has been trying to push, at the very core of its game mechanics (and they were aware of that since the very first game seeinf rhe beta sprite of Red with a whip) I'm still forcing these creatures into a ball, which gets easier the more damaged they are, and using them to do what I need, and even if they don't want to obey me, they can't escape. It gets even worse when you question their intelect but that's a whole other point. Even on the fprced captures, we have Ogerpon who literally wants to be your friend, but also Eternatus who was just a wild creature trying to survive but happened to have apocalyptic powers, but once you catch ot, it's over. No one will question your ability to have it (something than even the anime did!) because well, it's over for it. I can't do anything. Even on the Ogerpon example- had Kieran won, what would be the outcome? She would have been captured by force. Sure, she could have struggled...but so does most other Pokemon except the Legendary who quite literally chose you as its hero. And let's not even get to what the Terapagos scene implies, specially with how much more easily Master Balls are used on SV.
I know this is an extremely unpopular opinion that ignores other aspects of the franchise, but even back then, I remember telling N out loud "no you are right, you being manipulated doesn't mean all what you stand for is nonsense!" As the games point out, there are still abused Pokemon. If they can really be abused and asked to fight against their will, and in a world where Master Balls exist, how can I really tell N he doesn't have a point? It's one of those things you are not supposed to think too deeply on, because Blue should not take Oak's advice seriously if he still managed to become (at the time) the number one trainer on the world, only beaten last minute by the player. There are game mechanics that are that, mechanics, and should have never been questioned. BW1 for better and for worse did it, but they never had the guts to fully commit to me and 2 reduced it to "Ghetchis bad, liberating Pokemon bad" with ironically not a single shade of grey in there. But if you only ever play the main series game up to that point, N is right. You could argue that makes the story even more compelling but while I would agree, it also means the ending also never resolved the issue and instead went for a cheap discourse of "it was an evil plan all along!". So I really don't think the BW1 story was written as self critique, but more like the opposite, to adress what some people said ans keep saying about the nature of Pokemon (and yes I think they failed).