1. You aren't fighting the villain
In most Final Fantasy games, you spend a lot of time killing random bits of wildlife, but even the first game puts you front and center with your enemies fairly often. When you're dancing around in Gurgu Volcano, you're facing down the minions of the Fiends. More recent games are even more steady about that, with Final Fantasy XIII taking about half the game before you fight anything other than minions of your primary antagonists.
Heck, in a lot of games, you face the main villain more than once. Part of what made Final Fantasy VIII so weak thematically was that the writers didn't even bring the real villain onto the screen until you were almost done with the plot. You meet Vayne and Gabranth before you're even able to leave the first city in Final Fantasy XII. You face Kefka repeatedly in Final Fantasy VI. You even start Final Fantasy II by directly encountering one of your primary enemies.
Meanwhile, in the online installments, you... mostly fight other things. Your most frequently encountered enemies are either bits of wildlife or beastmen, and the games go to great lengths to make it clear that the beastmen are mostly victims. Outside of a handful of missions in FFXIV, you never encounter the Empire. You rarely directly encounter your enemies in FFXI, with the Shadow Lord being the only major opponent whose forces you clash with on a regular basis. And it's hard to really get a bloodlust up for those foes for the reason outline below.
2. A lot of the villains don't seem terribly villainous
FFXI's big headlining villain is the Shadow Lord. If you have somehow missed the game's story up until now, here's the gist: You find out the Shadow Lord is a Galka who was murdered because he fell in love with a Hume woman. He then rallied the oppressed and persecuted beastmen as his army, after having seen the ceaseless cruelty unleashed upon them by the three nations. (We're treated to a cutscene in which the future Shadow Lord examines a Quadav hatching chamber that's been smashed to pieces just because the explorers could do so, not because the Quadav had done anything.)
In other words, here's a guy standing up for several oppressed people and trying to lead them against a society that doesn't even try to communicate. And he's supposed to be the bad guy.
Some of the villains from the online games are satisfyingly evil. Even if you can understand Promathia's motivation, he clearly needs a good swording. But pretty much every major group in FFXIV is made up of warmongering jerks, and both the beastmen and the Empire are really looking for an excuse to kill each other. They sort of deserve what they get. Even the Zilaart have done a lot of good for the world; there's an unstated (and ignored) implication that killing them will have long-term ramifications for the world's political structure. You wind up feeling like a designated hero rather than an actual hero.
3. There's no personal stake
This is something that's harder to handle than other matters, but part of what made villains from prior games memorable is that they hurt the main characters in some way. Only in the original Final Fantasy do you not wind up losing something major to the villains, and some games get downright nasty in this regard. (I'm fond of FFX's wedding scene because of precisely that -- it's a very deep and personal violation, but it's not a violent death you get to avenge.)
Admittedly, it's really hard to set up that magnitude of loss in an MMO. But the games just don't even bother trying. Wings of the Goddess came the closest to giving players a personal stake, and even then it was limp. NPCs occasionally die, but they usually die as part of your victory, not while you're still knee-deep in struggling. There are no heroic sacrifices, no scenes in which you find yourself really losing big, just a certain guy propped up at the end for you to start hacking away at.
FFXIV clearly put an effort in to make you feel the sense of violation at the hands of the Empire with all of the loving details you get regarding Ala Mhigo. But you never get to go there and see what was lost; you just hear about it from people notably removed from the environment. Ironically, it might be only after the events leading up to the relaunch that players will actually feel as if the Empire took something from them. Of course, depending on your feelings regarding the state of the game, it may have taken something you were happy to give anyway.
Villainy is afoot
None of this ruins the games, but it does mean that any real nemeses have to be entirely player-supplied. It's a definite weakness, one that I'm hoping FFXIV's relaunch and FFXI's expansion address.
Maybe I'm wrong and you had some deeply personal stake in taking out Eald'narche's little floaty things. If so, by all means, let me know down in the comments or via mail to firstname.lastname@example.org. Next week it's time for a bucket list because FFXIV's doom is an oncoming freight train.
From Eorzea to Vana'diel, there is a constant: the moogles. And for analysis and opinions about the online portions of the Final Fantasy series, there is also a constant: The Mog Log. Longtime series fan Eliot Lefebvre serves up a new installment of the log every Saturday, covering almost anything related to Square-Enix's vibrant online worlds.