>>57619725Red explicitly dismantles Team Rocket and shames Giovanni into hiding indefinitely, even decades after his downfall.
Anime's Giovanni is still pridefully leading Team Rocket by the end of the Ashnime, because Red doesn't exist to thwart his plans, and Ash isn't roadblocked the same way Red was, so he never leads up to defeating Giovanni to such a degree that he's forced to disband Team Rocket.
Gary never takes over Viridian Gym in the anime, instead Agatha has to take over as a substitute while they scout out a new leader (and we know it isn't Gary, because he never mentions doing so even when he appears in Journeys, because he's explicitly a Pokemon Researcher unlike Blue). And even then, on the topic of bringing up Blue/Gary, if you insist the anime is canon and that Ash and Red can co-exist despite all evidence stacking up towards incompatibility, you now have to contend with the fact that Oak has TWO grandsons with identical appearances and personalities, and their only true divergence is name and occupation after they respectively mellow out.
Koga has a sister that neither he nor Janine mention in the games, despite the fact Janine made an appearance as an NPC in RGBY prior to taking up her father's mantle in GSC, so it shouldn't have been an issue for his sister to appear in the games as well.
Blaine's Gym in the games is a standard building, but in the anime it's built directly by terraforming the inside of Cinnabar Volcano itself.
Do I need to keep going, or...?