My issue is with Wikia as a company, not the wikis themselves. Their paid staff has too much of a tendency to stick their noses in and dictate how a wiki is run (though this is more prevalent on the larger ones), even when they have no interest in the subject of the wiki itself, and take no input from the actual users on any decisions they take affecting all their wikis. A good example would be when they rolled out their current layout a few years back - the vast majority of their actual users hated it, but it was designed to maximise advertising revenue, so they were never really going to listen to the complaints people had about it. They also don't allow the wiki's actual users to have any amount of control over the backend of the site, such as deciding which plug-ins they want to add or remove. What goes for one place is applied to everything, whether you want it on your own wiki or not.
I could go on and on about the issues I have with how Wikia (the company) conducts itself, but I'd rather not bore everyone here.
For what it's worth, I think wiki farms as a concept are fine if you just want to do something for fun, like the SB social wikia, since they do have the advantage of not requiring you to put actual time and money into getting it up and running. But I think for more serious ones, running them should be left up to the people who actually care about the wiki's subject matter, and not to someone who's paid to do it and probably has no actual interest in it themselves; basically, they should be by the fans and for the fans, not by the fans and for the benefit of some corporation's bank balance.
I co-own and run my own wiki myself (
Fire Emblem Wiki - which has nothing to do with Wikia), so it would be hypocritical of me to be opposed to the idea of wikis.