I think the most frustrating thing for a guild is knowing that there is an easier boss later in the instance, but they are having to decide to either drop progression on a boss, or skip ahead. Blizzard absolutely nailed this with Ulduar. The first boss was required, but then you had a choice of 3 bosses which you had to clear to move forward, which then opened up to 1 mandatory boss, and 5 paths of progression, ending with 2 "in order" bosses.
So basically in Ulduar I had the choice of going for Thorim, and then coming back for Hodir for the week. You can't do that in today's instances, you either have to kill it, or move on. ICC basically did the same thing with an opening linear style, then branched off into many bosses where you went Linear -> Choice of easier bosses -> Choice of harder bosses -> Lich king.
I really think Blizzard needs to return to this model, to allow the "casual / semi-hardcore" guilds a choice of where they want to progress without punishing them. Sure the linear raids have their place, and I feel those are much better suited for 4-6 bosses, but when you have 12(13) bosses it makes it very frustrating for the casual guilds.
My ideal setup is 3-4 bosses, with the 4th being mandatory to move forward, then 1-2 mandatory, then 3-4 more paths and finishing on the last boss.