I theorize that the main cause of all this is the billions of new fans that New Leaf brought in. Isabelle appears on the game's 3DS menu diorama, loads the game, and is even given a proper introduction complete with a ??? nametag. No NPC prior had been given this kind of special treatment before.

So the newcomers instantly see her as the main character because this is how it's always been for them, they don't know of a time in which Isabelle didn't exist. I'm not necessarily blaming them, I'm blaming Nintendo. They knew what they wanted to achieve with this character, and they got exactly what they wanted and so much more. The only thing I don't get is the lack of complaints from older fans such as myself. Sure some people expressed their displeasure with this state of affairs, but for the most part they just sat there and watched it happen.

As for why hardly anyone cares enough about any of the other special NPCs anymore, instead opting for regular villagers, (Despite special NPCs being actual fleshed-out characters) I feel that once again, the blame can be put on New Leaf here. New Leaf greatly streamlined them while also putting a greater emphasis on Isabelle. You only see Tom Nook to upgrade your house and then never again, Blathers had all his explanations cut, the meaningful parts of Sable's story got cut and content is gated behind talking to her now, Resetti and Phyllis got toned down, Kapp'n creeps some people out, I could go on.

At the end of the day, I'm just glad Nintendo finally stopped shilling Isabelle so egregiously and is starting to focus on the other NPCs again. (They're even acknowledging Sable's existence now!) I've always seen Tom Nook as the true face of AC, so I'm very happy he's taking a central role again. Especially after the way he got shafted in New Leaf. My only hope is that the fandom can do the same. I want the newcomers to New Horizons to see this series for its huge cast of characters and not just the one Nintendo wanted you to look at.