@Mike
It actually has almost nothing to do with setting up a story. That's just the excuse for the public. My guess is it has a lot more to do with making each content patch have something for everyone. 3.2 (ToC) and 3.3 (ICC) had new 5mans along with the new raid tier. 3.1 did not. As a result, I'm sure most people who don't raid had no idea what the whole Ulduar thing was all about, nor would they have reason to. Releasing 5mans with each raid tier makes the content patches seem more well-rounded. My guess is they decided to just take 2 instances Cata was going to ship with and move them back to 4.1 to round it out.

@DarkFinch
4.1 is to Cataclysm as 3.1 is to WotLK. In other words, would you have assumed that most players would not have been level 80 and ready for heroics by the time Ulduar had come out? Player will be more than ready to run heroic instances well before teh second tier of raid content is released, or at least I damn well hope so.

@(cutaia)
I can get behind this reasoning more than any other justification, but I still feel they're padding their future content patches by holding on to already (or nearly) completed content.