They're right that open-endedness harms the quality of the main plot because with open-endedness comes not only the destruction of canon (since no one can say what the "true" series of events is), but the additional workload on the author to write for every possibility, and the need to structure events in such a way that they can happen in several chronological orders, which makes transitions awkward and sudden.
Players don't need any assistance creating their own stories. In fact the best player-created stories come from games that have no plot whatsoever. When a developer wants to tell a story, they need to put their foot down and say "Listen up, this is our game, that means it's our story, and we even built this whole game around it, so stop whining." That's how books have been doing it for millenia and humanity hasn't gotten bored with them. If the player wants to make their own story, they're reading this, so they have access to a perfectly good computer. Get typing.
The real problem with jRPGs isn't the linearity. It's that they HAVEN'T HAD A STORY WORTH TELLING IN OVER A DECADE. It's not that your storytelling methods suck Square, it's that the stories THEMSELVES suck, and the characters in them even moreso.
I was really hoping FF12 would be a sign that the rapid downfall of jRPGs was nearing its end and the flagship franchise was finally starting to get their sense back, but people like me, who want adventure with brave heroes and hateable villains seem to have all moved on. Ever since their ill-fated decision to allow Nomura to design characters for FF7, Square fandom has been plagued by weeaboos and otaku who want nothing more than pathetic main characters that give them false hope that they can ever do anything worthwhile as they are, villains that turn out good, because maybe all those mean bullies in middle school were just "misunderstood" and didn't mean what they did, and female characters that exist only to constantly support protagonists that any real girl would've been abandoned as the useless sacks of angst they are long ago.
A protagonist that acts as our frame of reference to the story without dominating it, and knows his place in a group with people far more relevant to the plot than him, offering advice when he has it (and it's good) and then shutting up and letting the important people talk? More importantly, a protagonist that's looking for the same thing any decent gamer is: adventure? Five out of six characters that are relevant to the plot? Writing that isn't groan-inducingly sugary and forced? A combat system that actually rewards cleverness (gambits) and reduces tedium(auto-attack)? A villain that isn't an alien, metaphysical evil force, or all-powerful magic-wielder? A villain that's ACTUALLY KIND OF A JERK? And he isn't trying to blow up the world?! And best of all, NO FANFICTION-QUALITY ROMANCE SUBPLOTS?! FF12 was the best FF since 6, easy, and look how the otaku responded.
Maybe one day, when the weeaboos go extinct (from not breeding, naturally), somebody will put Square back on the right track. Until then, if you have a single shred of integrity, don't even bother.