FRLG differences are irrelevant so either or on that one although they would be more likely to be the basis of any lore since the Sevii Islands offer more than anything RGBY or LGPE do.
HeartGold makes more sense than SoulSilver although Crystal is also accpetable imo, the reason being is admittedly very minor in that it makes more sense for the Kimono Girls to regard Ho-Oh as their patron deity than Lugia due to the proximity the former is to the Kimono Girls and their attire as well as the general style of each location.
Emerald is the easiest way to refer to Gen III since it plays out essentially both scenarios although the only trade-off is anything that was added in ORAS which can basically be boiled down to the Delta Episode, so... yeah Emerald is the best source by a long shot.
Platinum seems a lot more in line with Cyrus' ideals in the need to create a new word requiring both time and space also having generally the most complete dex helps.
Imo Black and Black 2 would be the canon of the Gen 5 Games since I think N much more aligns with the concepts of ideals rather than truths, it was his ideals of freeing Pokemon from a misguided entrapment that shrouded his ability to see the truth behind Ghetsis' motives, that being said the thing with White 2 having the old ruins beneath Route 4 is fairly reasonable although so is Black 2 having a developed area along that Route given the massive cities of Castelia and Nimbasa.
Y certainly makes more sense as the canonical of Gen 6 given the nature of the Fleur Cannon, given its primary function was death. As for Gen 7, I would honestly disregard USUM because their story is completely fucked in terms of plot explanation with screwed up character motives galore. Between Sun and Moon I would be inclined to go with Sun simply because Solgaleo strikes me as the more befitting form for Nebby to take.