Canon Line:
Gen I/RBY & FRLG: First off, we already know Let's Go takes place in its own continuity so we can place it side. As for Gen I, a thing which I'm going to believe is that the "default" canon is a mixture of all the games and, as long as nothing conflicts, there's no reason to assume it didn't happen. So, in this case, I think we can take FRLG to be the most "canon" of the Gen I storyline BUT we're going to take the element of Yellow where Red starts out with a Pikachu and gets the other Kanto Starters. "So does that mean Blue got an Eevee in default canon"? Eh, maybe? Honestly Blue's Starter doesn't seem to matter as he never uses the Kanto Starters or Eeveelutions past Gen I. And let's not even get into the status of Green/Leaf...
Gen II/GSC & HGSS: This one is even easier as HGSS includes the Eusine & Suicune subplot from Crystal on top of the additions it made. The only major difference in these games is what order you awaken the Tower Duo, and for canon purposes that doesn't really matter. In fact the knowledge the player even did that would only be known by the player (and the Kimono Girls in HGSS), so that's probably not even noted in canon.
Gen III/RSE & ORAS: AND now we come to our first major canon knot. Before ORAS it would be easy just to say that Emerald was the de facto canon default. In honestly I would still say it is. However that canon now has the additional stuff added in by ORAS such as the clearer goals of the villain teams, Delta Episode, and Mega Evos. So to combine this jumble together: Both Team Aqua & Magma awoke their Legendary, they appeared in Sootopolis to battle, Rayquaza quickly showed up to quell them, one left while the other went to the Cave of Origin and used its Orb to Primal Revert and battle the player, Steven was acting Champion though soon Wallace takes over (though I can see the two swapping the titles every so often and handing it over if the other has something else they want to do for a bit), but before then the Delta Episode occurs. The only major gap in this is which Legendary appeared in the Cave of Origins, but honestly that specific detail doesn't matter and can easily be written around. All that matters is that one of the Legendaries appeared in it and Primal Reverted (heck, if they really want to stretch it, they could have it both went to different inner chambers of the Cave of Origin and that both May and Brendan took on one of them). Oh, yeah, I guess whose child May and Brendan are would also be a major important difference; if anything it seems like Pokemon Masters has chosen Brendan to be Norman's son and May is Birch's daughter. Though that is a very specific piece of information that 99% of the time doesn't come up and if it does can likely be glossed over.
Gen IV/DPPt & BDSP: I think there's no problem with just throwing out BDSP as it's just a SUPER direct copy of DP and Platinum I would consider the canon default for all the story inclusions it has, especially with Giratina and the Distortion World (and that Cyrus captured both Dialga & Palkia). Only major difference not resolved would be who was the role of the player (and child of Johanna) and the other being the Professor's assistant. In Masters its mentioned Dawn is the player (& Johanna's daughter) while Lucas is Professor Rowan's assistance. Though, once again, super specific so most of the time ignored or glossed over.
Gen V/BW & BW2: HAHAHAHAHA! Good luck resolving this! We got two (possibly three) main problems here: N's dragon and the player character (and maybe the player character of BW2). Like, they would have to remain SUPER obtuse and try to change the topic so no questions was asked. "And then N and the other chosen one had their dragons fought, with the chosen one being the victor". "So which dragon belonged to whom and also who was the other chosen on...". "... AND then N left to do some soul searching, the other chosen one went to look for them, and Iris became Champion. Anymore questions? No, good!". Master seems to hint Zekrom was N's dragon & Hilbert was the player in BW (though Master oddly doesn't take a stance whether Nate or Rosa was the player in BW2, aside Rosa having the Snivy family and Nate having a Braviary).
Gen VI/XY: Now at first you'd think it would matter which Legendary was the one Lysandre used, but not really. You can just have it so Lysandre caught both and it took the combined efforts of Calem & Serena to beat him (and it barely matters which one was the player and which was one the Rival as, in terms of canon, both come off pretty equal by the end of things).
Gen VII/SM & USUM: *Low grumbling noise* As MUCH as I would like SM to be the default, most of USUM's story is likely the default here. NOW, I would say there's no reason that SM's Ultra Beast Hunt and USUM's Episode R couldn't have both happened, but USUM's additions pretty much mean that Lusamine never goes Mother Beast (and thus Lillie never leaves to Kanto to help her, instead Gladion leaves just to become stronger). I guess separating my feelings from the Gen VII's story that is the best outcome overall as Lusamine is up and active and no longer crazy, but it's also a bit of a hit to Lillie's character. Now whether Nebby evolved into a Solgaleo or Lunala I think can be wrote around, especially since the Ultra Recon Squad had the other Legendary (actually they have both) so both a Solgaleo and Lunala were present when Necrozma attacked, it absorbed one of them, the other rode the player to them to the Ultra Megalopolis, and the player defeated Ultra Necrozma freeing Nebby. BTW, Masters also seems to have ignored taking a stance, while she does have a Lunala in one of her special outfits its apparently the Cosmog the player got from the Lake of the Moone/Sunne. She mentions Nebby but only says it's with a good friend she trusts... even though both Elio and Selene are on Pasio (and dialogue from Elio seems to suggest her was the player character as he mentions trying to help Lillie and her worrying about them).
Gen VIII/SwSh: Since both the player and Hop use the Hero Wolves to save the day there's really no major canon issue unless you specifically go into (1) what wolf Hop has and (2) the identity of the player. Identity of the player can be easily written around, but Hop's wolf? Will only be an issue if Hop makes an appearance where you battle him.