I really, really want you to elaborate on this point considering by the time I finished my recent XY replay my opinion of the story absolutely tanked. I'm not mad at you, hell I legit admire people like you who are able to see something in media or components of media that pretty much nobody else can, and that's why I'm so curious to know your reasoning in greater depth.
My apologies for the tragically delayed response to your perfectly understandable inquiry to my contrarian position.
First, some backstory. I entered into the Pokemon fan base about two years after it invaded the shores of America. Thus, I grew up with Generation 1 (151!) as my main influence. Now at the time I didn't have a GameBoy system. My parents prohibited such devices. So I spent my Pokemon journeys in my backyard using my imagination to catch my party and defeat Team Rocket. (Undefeated record, btw. I knew my types. Complete Gary-Sue as a protagonist). I collected the cards, plushes, assorted food products. Remained steadfast through Gen 2 but slowly fell out by Gen 3-4. My grandaunt still gave me cards but I specifically despised the new card design and inflating HP/attack damage. So without video game systems and the card, I slowly lost interest.
Fast forward to college. A fellow student on my floor was into Pokemon. He asked me for my thoughts. I told him that I used to be a huge fan. He told me to watch the XY anime. I figured why not? So I did. Nice piece of escapism entertainment and I remembered why Pokemon was awesome and enjoyable. Needless to say, the Gen 6 Pokemon made a huge impression. I entered into the Disney College Program and for my birthday a fan from college sent me a 3DS with Pokemon Y. (I had played LeafGreen, Crystal, Emerald on an emulator by that point along with Yellow on a GameBoy a high school friend gave me). I would play Y on the bus while commuting to work. It felt like the perfect video game. A group of friends that would drop in and not stick around like glue, an assortment of new Pokemon that weren't locked behind postgame walls, a solid level curve. A stress free game at a time where the DCP (highly anticipated) turned out to be disappointing.
I understand the complaints about XY and perhaps if I came from Gen 4/Gen 5, I might think the same way.
For example, Diantha not helping out against Flare is seen as a negative. For myself I don't care. I am the hero of the story. At the end of the day, the game will have me save the day. It is irrelevant in my eyes if the Champion helps with the Electrodes or not. Because at the end of it I will be fighting the Big Bad. (If it is different in S/M and S/S, let me know. I still need to finish Sun (cut scenes killed my drive) and I still need to purchase a Switch. Life has been too busy to justify the expense. Hopefully, it slows down soon.)
Overall, Diantha has what I like in a Champion; engaging personality, killer looks (I am not mainly a legs or short hair guy but she pulls it off probably because she has that whole old school, 1940s Hollywood glamour) cool team (Hawlucha fan in the house), and isn't shoehorned into the story only to take a backseat at the climatic battle for no other reason than "oh yeah the PC has to save the day."
Same thing with Team Flare. Is their plot inherently ridiculous? Sure. But that is standard for Pokemon. Team Rocket inexplicably invaded the whole of Saffron when they only needed to strike at Sliph, Team Magna/Alpha want to wage eco-terrorism using legendaries, Team Galactic's leader wants to create his own world without feelings, BW tries to address the core tenant of the franchise but backtracks at the last minute with the copout of tyranny.
As for Lysandre, I found his arc intriguing. How does a humanitarian go from wanting to help the world to deciding it is irredeemable? To save the world he has to destroy it. It actually has become more and more relevant especially in light of recent events. That belief fascinates me. A man becomes so desperate for beauty and goodness that revisionism is the only answer. He correctly understands that there are givers and takers but his extremism blinds him to the morally right response.
Is it strange that Lysandre had an entrance fee for Flare? Yes, but I thinks it works. He is a hypocrite. Most people of his ilk are. He wants to remake the world. There is no shared belief on how that it is to be achieved.
And the nice added dimensional of having a Mega Gyarados. He is utterly insane and wrong-headed but he is not incapable of kindness.
As for pace; well, outside of the gap between Gym 1 and Gym 2, everything flowed well. I thought the Gyms and Routes were never too long or too short. The caves weren't overly annoying (hello Seaform) and I enjoyed the scenery.
I think overall Gen 6 felt like an updated version of RBY/FRLG. A brisk game that allowed me to play without being bogged down in overly complicated plots or not being able to find the Pokemon I like. My dream team for XY was Greninja, Sylveon, Aegislash, Talonflame, Vivillon, and Hawlucha. And obtaining all of those Pokemon was a breeze. I can only imagine how the GSC/HGSS template would have handled them. Sylveon would have taken forever with the heart metric (it was swift in XY), Aegislah would have been locked for postgame, and Hawlucha wouldn't have been available until after Gym 7.
For the TLDR crowd: My Gen 6 love mostly has to do with my personal relationship to the franchise. Is it the most rational position? Not really but desire rarely is. I love the Pokemon, I love the characters, and I mostly love the story. Even if it is based on France (don't tell my English ancestors. My Scottish ancestors don't mind since the Auld Alliance was a thing.)