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People don't just inherently hate humanoid Pokemon, it's usally being humanoid and being fucking ugly, which is what Incineroar is.
Its a cat for 2 stages then turns into a bipedal "tiger" that's really just some guy in a suit with stupid proportions and ugly sausage fingers. The combination of the design whiplash from Torracat to it just being unappealing is why it gets so much shit, Samurott is also a victim of this but he's not as offensively ugly, or as shilled as much as Incineroar so he's not brought up as often.
The point you're making with waifumon would only be valid if their first stages were completely different aesthetically from their final stages, as in, if Bounsweet were some fish or of Ralts were a dinosaur or some shit.
