The story is great, but it blatantly gets in the way of the rest of the game

[Xirean]

This is a lazy argument. This is literally the only RPG in existence where progression and story don't flow together seamlessly and back each other up, but instead get in each other's way. That is the criticism I have for this game, and I'm not going to accept "If you hate that the story and the progression fight each other you just don't like the story enough" as an argument for why things should be that way.

It's a massive flaw in the game. There is no other RPG I can think of that has this problem or where this would be acceptable.

I'm confused how the two fight each other. Can you explain this?