Yeah, I do feel this is being blown a bit out of proportions.
All fandoms have these recurring themes in some way or another, it's basically unavoidable when one pours so much feelings into a product only to find someone else with the same exact amount of emotions into a completely different outlet, ensuing the flame wars and clashes between factions.
This will keep happening as long as fandoms will keep being left to their own devices, with no one to look into the matter except to bring them back just to complain about how bad they are.
This is hardly any different than "KH II system vs command system", "Faulkner music vs original score", and so many other examples. Just the other day I've found out there are clan wars over this or that Dragon Ball manga artist. I don't think they are the worst thing that ever happened to their respective medium.
Heck, I think "fandoms are ok vs fandoms are the scourge of the Earth" is another fitting example.
At the end of the day you can just accept that someone will feel differently from you and that their complaints doesn't take anything away from your own taste and enjoyment of the same product. Don't go where people say something that really bothers you, and don't engage with them on that subject if you feel you or them can't handle a civil and productive exchange. I avoid any video about something I like labeled "[Name]: why it SUCKS" for this very reason.
Onto this specific subject: Final Fantasy applied sometimes drastic changes and the saga carried itself over many years, years in which players, directors and the videogame industry changed. It's only logical that there will be some people that love an FF titles while hating another one, I'm not an exception: the FF XIII trilogy represents to me one of Square's most colossal failures, with close to none redeeming features whatsoever. It's one (but not the only) reason why I refer to that period as the videogames' Middle Age. I would definitely put it above the FF VI - FF VII debate as some of the worst things to have ever happened in my personal list, lol.
You don't have to come shouting at me about how wrong I am: some people love it, some people think it's the best FF ever. It's cool.
It's also cool if you think my favourite titles (IV, VII, IX) are the worst of the franchise, and I'm willing to go over their many flaws. None of this really damages my relationship with the series as a whole.
In order to engage with people and fandoms you'll have to come to term that the mere concept of someone liking or disliking something shouldn't bother you.
I know it's not easy, btw. I'm not saying "come on, you should do this, DUH": just looking at, well, the Internet it's pretty self-explanatory how this is absurdly hard to do for some.
And people will do much more than just stating their opinion, in many instances they will manifest their worst behaviour. All the same: try and learn to ignore them. The only other route would be trying to force them to think that way, and before being morally debatable that's just impossible to do.
BTW, this should go without saying, but that doesn't mean you should ignore anyone who has a different opinion either: discourse is at its best when made by people with different viewpoints who can engage in thoughtful discussion. Just ignore those people (or those opinions) that you think you cannot handle. Your well-being is worth way more than trying to establish where a videogame ranks.