Biggest flaw i could pick with Pokeshipping is simply the inconsistent nature of the show. Ash resetting as a character damages Pokeshipping considerably every time it happens.
On top of that it's Ash's sexual inconsistency. Misty has a clear 1+2=3 response. Flirt with Ash and she gets angry, Ash goes from explicitly being attracted to women to having a typical childlike belligerence to just not responding when girls flirt with him directly without ambiguity.
This ship could work perfectly fine on paper, it practically writes itself, but it seems to be a poor fit for how this franchise wants to be. It begs for a payoff it cannot have
And yes, 4kids having absolutely no self control when it comes to marketing their relationship caused confusion in the long run, even if they didn't create it.
It also seems like the only reason these two were allowed to touch each other/attempt violence so often was because the show wasn't as iconic. It didn't have a big image to uphold yet. This was an era where james could wear fake tits
Amourshipping has similar but opposite problems. The anime's status as an advertisement was well established, kickstarting such a strong romance beyond that point is shakey. Couple that with it being set in a series that already played with the idea of an Ash Ketchum romance and you essentially have a story arc guaranteed to alienate a large number of previous viewers.
Ignoring the baggage and looking at XY in a vacuum, Ash's obliviousness goes from being a cute character trait to an annoying cliche. It becomes difficult to take the ship very seriously when it's an immovable object meeting a rather stoppable force. At the very least Ash reciprocated Misty's behavior towards him, bickering, mocking, even swinging at her once. With Serena he seems to max out at grabbing her hand and being nice to her, something he did with Misty. They should have given more.
I would love to speak on Pearl, Advance, and Negai, I would have to rewatch those series.