The only thing I can contribute to this conversation is my experience playing the Final Fantasy MMOs. I never knew too much about the Final Fantasy lore to say whether XI or XIV were close or a departure from the series. My friends who play those MMOs with me are HUGE Final Fantasy fans and one pointed out in the case of XI was if you replaced the airships, chocobos, and the job names all with something else, it could just be an MMO unrelated to the Final Fantasy series.
I started XI during the US launch in 2003. It was my very first MMO, but I enjoyed it a lot. I only recently put the game down for the last time and closed out my account, but I was very active right up until the end. XIV, I also started at launch and continue to play to this day -- though only for a few more days until it goes down for the up and coming relaunch. It was my understanding that XIV was a little closer to the FF lore than XI was and given the upcoming 2.0, or A Realm Reborn, players have been saying it's looking to be more FF-like.
I can't really say that bothers me too much, because as MMOs, I enjoyed them a lot. But like you said, I was always aware there was tons of backlash towards Final Fantasy jumping into the MMO arena.