a) Nobody's computer has enough RAM or processing power to do one flash an hour long and have it stay in sync and not crash. Flash may seem like it can do anything, but one thing it continues to suck about is how long a flash animation can be. You can make a game that lasts an hour, but the flash virtual machine itself sucks greatly at keeping track of resources after a while.
b) Flash is vector based, an hour long flash animation wouldn't necessarily be huge in download, just a lot of processing power over time.
With the exception of south park the movie, I don't think anyone is willing to sit through an hour of poorly drawn, poorly orchestrated, poorly voiced animation in one sitting. Broken up over several pieces so you can stop/pause, get up, get a snack, use the potty, grab a drink and come back.
People are willing to watch Bonus stage 3 episodes at a time, not 20 at a time. Hell even when I watched it, I thought it was terrible and only came back to it after watching one of the multi-part episodes, when I then gave it a second chance and watched it from the beginning. While it's not the worst animation ever, it's -VERY- hard to get into if introduced through the beginning. That's the risk you take when you base things "getting the reference" to it.
One of the reasons I haven't watched space tree is that it's just so boring, it's talking heads. BS and EJ&B are more than just talking heads. Flash is good at doing "talking heads" because it's very easy and requires no additional creative skill. An hour of "talking heads" is not something I can stand to watch. It's also the same reason why I don't like sprite-rip comics/animations. The same 4 stock images with flapping lips is not very exciting.
Regular non-animated webcomics are also pretty hard to read through in one hour, comics that use primarily the same side view or 3/4 view for all their characters that look nearly all alike become boring to look at. They read fine when you read them a couple at a time, but feel like a chore to read the entire archive to get whatever joke happened in the latest episode.