"I like the idea of using skill challenges that are integrated into a dungeon crawl, but how do we get out of just making them perception/trap removal checks?"
Thanks for your replies and your ideas. I think the most important part of integrating a skill challenge into a dungeon crawl is to know up front what you want defeat and victory to mean. If defeat means they lose or can't access their way back, while victory means they... well, don't, then Dungeoneering and Athletics become important. If defeat means that otherwise neutral dungeon denizens become hostile, while victory means they provide aid, then Diplomacy, Bluff, Intimidate, or certain knowledge skills could be useful.
And even just making Perception and Thievery checks could be interesting, given the new philosophy of making traps part of encounters instead of encounters on their own. Just checking every door is boring. Deciding whether or not to pull the rogue out of combat to disarm the trap that's doing poison damage every round while the skeletons close in is interesting.
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