Just a few last thoughts, and clarifying points.
I do tend to buy into the idea that the popularity of the JRPG genre in the west, largely revolved around Final Fantasy, so restoring Final Fantasy to a greater degree of popularity would go a long way towards fixing the perception that the genre in floundering. Final Fantasy itself, however, has suffered from a few problems in recent years. The two biggest ones, being readily obvious in Final Fantasy 13.
The two problems were, in short, that the game both suffered a severe identity crisis, and, for the most part was actually a step backwards in terms of storytelling.
The identity crisis is obvious. This was an RPG, that didn't want to be an RPG, but didn't know what else it could be either. It jettisoned major aspects of traditional JRPG gameplay, and replaced them with either broken systems or nothing at all. There was no real item management system, equipment could largely be ignored through much of the game, there were no real towns or NPC's, and the overworld were even more linear than the already horribly linear FF10's. In short, it felt less like a role playing game, and more like an event playing game, and I'd attribute this to the designers not actually having a clear vision for which direction it actually wanted to go.
Then, there's the story. To be blunt, I know people who beat the game, and still have no idea what the game was supposed to be about. The plot was full of self referential terms that made zero sense to the audience, and therefore most individuals never had anything beyond a vague notion what the core plot was supposed to be about. So instead the story would've had to have relied on the characters, but ended up failing here too. As another commentator pointed out, the game really did feel like bad anime fanfic. Most of the characters were direct copies of common tropes in anime, and some were even direct retreads of characters the FF13 development team created during FF10. I'm sure I'm not the only one to notice how many similarities between there were between Vanille and Rikku.
In essence, the story was far below the expectations of fans and consumers, and this hurt the franchise considerably. Perhaps more than any other JRPG franchise, Final Fantasy had to grow and become more mature with the audience, and instead we got a title that was more juvinile, and more clumsy than any entry in the franchise before it.
All this said I'm actually somewhat optimistic about Final Fantasy in the long term. I think Square has at least learned some lessons off 13, and how that the trilogy is about to be over, we can finally wave goodbye too that flawed storyline for good.