Try also the fact that it had...
- Character deaths
- Character plot twists
- Constant villians from start to finish, and those villians actually disliking each other, meaning there were occasions that you would "team up with the enemy".
- Effective comic relief
- More than six playable characters
- Unlockable characters
- Non-humanoid characters
etc.
The plot and characters, while not perfect, were intriguing to people who wanted more than a Disney "all the good guys live" situation.
If, in FFXIII...
- Sahz actually killed himself
- Hope actually succumbed and turned into a Cie'th, thus having to be killed
- Jihl ended up joining the good guys at some point, after seeing the enemy for his true colours
- The final boss was Barthy
- Barthy was more prevelant and his reasoning for doing what he was doing was better explained, and his "co-conspirators" were better fleshed out
- There were better minigames with good comic relief
- You could unlock additional characters
- A non-humanoid character of Pulse joined the party
...it might have been received a lot better. Especially the first parts. I mean, seriously, they would have blown some people's minds (excuse the pun).
As for SE thinking people don't like JRPGs - I don't think that's the case. If you mean traditional JRPGs, 2D etc, then I think that's because the audience is actually quite low for them. While Bravely Default did well, it perhaps could have done a lot better. Maybe it will in time, but the general feeling from me is that it's still not numero uno for them. My feeling is that they feel JRPGs don't do well because no JRPG has done notably well this generation from any developer that isn't Square Enix. The closest is probably Ni no Kuni.