Dueg is the first blogger I've seen to suggest this, but I feel like it's an undercurrent that's been going around since the 3.1 release last week (and we'll probably find out more when Guildwatch comes out later tonight). He suggests that Ulduar might be, of all things, a guildbreaker. Now certainly it won't be nearly as much of a roadblock as Karazhan -- not only was that a tough instance, but it was also the first one we came across in Burning Crusade, and guilds who couldn't make it in Kara had no place to turn back to (at least guilds that can't make it in Ulduar can fall back on Naxx farming). But there's no question that Ulduar requires some excellent gear and some serious tactics, and if your guild has people raiding who are missing either one of those, you're going to be hitting your head on the wall quite a bit in there.
That's not to say that it's super hard -- it's not, especially if you know not to stand in the fire and you've got the kind of gear on that lets you conquer the Heroic achievements. A lot of guilds have 25 of those people, and they're doing very well in Ulduar so far. But as Dueg says, Naxx is a casual instance, and Ulduar is not. In Naxx, you can get away with losing a few people, or having a few folks in greens along. In Ulduar, you can't.
It's not the apocalypse for guilds -- most guilds will go back to Naxx if they have trouble in Ulduar, grab a few more epics and tier pieces, and try again later. And some probably won't bother with Ulduar at all -- my casual guild is having fun just taking our time finishing Naxx wing by wing. But Ulduar seems to be where the rubber meets the road with casual raiding. If there's a guild out there who has a few lesser raiders carried along by a few high-level veterans, Ulduar's likely to cause some friction.