I hypothesize you weren't around online as much during 2006 to 2012.
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They did it because the length of the MSQ was getting far too long for players new to the game. It was a bit daunting to think there was so much story to have to play through to get caught up with friends.
Finishing the story arc allows them to create a new starting point for players to jump into the game without having to go through 90 levels of MSQ to catch up to long time players. Likely for the next couple of expansions, players will have a choice to start a new character at level 90 and the new story, or start from level 1 and the original ARR story.
Where have you gotten this from? The conversation is about FF12. You know? Vaan, super political story, Fran fanservice, all those things people hammered for quite a while a decade ago?
Also, isn't FF8 also considered unpopular due to its gameplay and confusing plot past CD1?
FF9 does have its detractors, but it's generally received well for having returned to FF's roots both in setting and gameplay, especially after FF8 showing up with its weird junction system.
Whether FF10 surpasses 9, I can't say, both are generally favoured over most FF games as far as I've seen.
xD Oh but that isn't a flaw of the series imo. That's a flaw of the playerbase. People just expected future games to be the same as before, but FF almost never was that. Closest I can remember to two games being so similar were FF3 and FF5, with 5 expanding on the Job system. There isn't a singular grand unified version of what "Final Fantasy" is in terms of plot (you have comedy stories, depressing stories, invigorative stories, emotional stories, futuristic stories...), setting (medieval, cyberpunk, dieselpunk, steampunk, tribal, generic North Indian) or gameplay (ATB, CTB, RTB, ADB, Active X...). What tends to make a game part of the series tends to be certain tropes, certain characters and especially certain motifs. And it's up to each game to apply them as they see fit, even even omit them whenever unnecessary.
Heck, sometimes it's all about the label more than the game itself. That's how we ended up with FF Tactics xD it's such a clear reskin of the original Tactics Ogre, and while it reuses Cloud and some skills, most of it was pretty jarring given all the games released until then.
FF8 was received well by critics and had high initial sales, but it lacked staying power. Much of its early success is noted to have been a direct result of Final Fantasy 7 having left such a good impression on players. The junction system was the aspect of the game to receive the most criticism. The handling of Guardian Forces (summons, for those who might read this and haven't played the game) wasn't overly well liked either. The game's a little more fondly remembered these days.
FF9 sold far less than Final Fantasy 8 both initially and overall, but much like FF8's success was due in large part to FF7, a portion of FF9's failure to move copies was attributed to the impression left by Final Fantasy 8. Much of FF9's criticisms were aimed at its weird discount junction system as well as how new skills (and summons) were learned. People didn't particularly like Trance at the time either. The few fans aware of it at the time also heavily disliked the fact getting the best weapon in the game (Excalibur II) required you to sacrifice pretty much everything else.