They shifted to 3d with their first 3ds title. There's a connection there.
3D models *shouldn't* be a problem for keeping the National Dex, gamefreak are just ridiculously under prepared. Pokemon aren't complex shapes, a high poly models could have been created at any time in past 10 years, scaled down to work on the current console hardware, and still be usable for years to come. The same models could be used throughout dozens of games, so it's not like it wasn't worth the time investment, they just clearly didn't bother.
But even the X/Y models are good enough.
Is that model blocky? Can you see any triangles? No it's fine, the only thing that makes it look "last-gen" is the texture resolution and the games lighting.
They already have suitable models, even if they don't have models of a higher quality stored away (Which they should. Creating higher quality models than will actually be used in game is standard practice, you scale down the polygons/detail to work, you don't create the model at the exact detail you will use in game.) these models are good enough, even with the lowres 3ds textures they're still good enough, and I think pretty much everyone would prefer that they just used the models from x/y rather than just not put them in the game.
3D isn't a problem, and I do prefer it to 2d pokemon games tbh. I'm sure others like the sprites though.
If it's a choice between Sword & Shield being 2d and having all pokemon or Sword and Shield being 3d but having less pokemon, I'd still pick 3d.
