WoW's got enough of a history to be a good example of why we don't have long, branching dungeon in modern MMOs.

Maraudon.

Temple of Atal'Hakkar (aka Sunken Temple).

Blackrock Depths.

It was very difficult to get a group of players able to stay the entire run and even harder to find replacements when someone had to leave. The number of completed runs compared to runs started was very low as a result, not because of difficulty but because of time.

The same dungeons are also a good example of why dungeons end up with linear routes instead of branching paths. Too many players would get lost and confused, unable to remember how to get to the next boss. I spent a lot of time in Sunken Temple because I knew how to navigate the place without getting lost (and knew the statue order for the summoned boss) so others were always asking me to run it with them. Groups that didn't have someone who knew how to get around in there inevitably fell apart, which became a source of frustration and discontent.

The Thousand Maws of Toto-rak here would be a similar example. I've heard nothing but horror stories and hate for the 1.0 version because of the maze it was. Even now players continue to complain about how long the dungeon takes to finish.

I can understand why the makers of modern MMOs aren't wasting development resources on that type of content, as much fun as I personally fine it. They want to be making content that a greater portion of the player base would enjoy.

Before you say "but Ultimate is only getting done by 1% of the player base", Ultimate is also primarily put together from reused assets and generates considerable publicity within the gaming community due to the difficulty. Long branching dungeons wouldn't.