I think it's mostly due to the difficulty of managing reply threads with large groups of people. Most don't have the patience to deal with it.
And while I quit Facebook a year or so ago, I do think they serve different purposes. It's more like a webforum or something in the Reddit/HN vein. You can have one-on-one or small group discussions, but you can also post things out to your larger friend/fam/acquaintance network or to more public groups.
There's definitely something to be said for that, and as someone who spent my college through adult life on IRC and message boards, I get the appeal. I just wish it didn't have to be a winner-take-all situation where the "winner" happens to be a really shitty company I don't want to do business with.
The UI, mostly. Email threads are harder to read than the same thing almost anywhere else. And yeah, spam doesn't help—most people don't know how to set up filters and automatic categorization and such, even in programs that make it fairly easy.
Facebook's great use case is in maintaining casual communication with large groups of friends and family, friction-free, without having to fuss with mailing lists or spamming people with Reply All.