Eh, maybe I'm in the minority but I've been running my 4e campaign for a while now and based the overall campaign on the happenings in KoTS and Thunderspire Labryinth with them now taking on the Pyramid of Shadows. We've been fine, and had fun, but I have done the following:
1. Inserted the stuff into my world and not based my world on the stuff.
2. Upped some of the damage or some of the numbers of the enemy to keep encounters challenging.
3. Looked at the upcoming modules to more heavily integrate them with each other.
You know, the things most DMs do and the reason why any module from a publisher can be a bit less than wonderful. The utility of being able to pull a module off the bookshelf in a pinch is what I'm paying for in my opinion, not magnum opus storytelling. That's my job.
Though some publishers who more heavily focus on modules will always do a better job, that's not what we should be judging WoTC by. The fact that there's a market for better worked modules is what allows those other companies to operate and a good thing.