I guess that's why I never has any issues with KoS (I'm even fond of it). I never runed it as intended. I scrapped some battle encounters leaving only those I felt contributed to the plot I was creating at the moment. Yet, this also means I've had to put some effort to improve KotS.
The problems with it can probably be traced to it being the first published adventure for 4e, so it was new territory for both designers (who wouldn't know how to best use 4e's features) and DMs (who would go "New game, let's see how the intro adventure works out." and run it pretty much as written).
Hmm. Now I kind of want to see how Keep on the Shadowfell would work if translated to 13th Age.