Hi Jason,
I have a great chipotle rub recipe that I have used several times on pork. It is true that the smokey flavor of chipotle is mostly masked by the smoker, but there are other qualities of the chipotle pepper that give the meat good flavor as well as a little bit of heat. I have been able to taste the smokey flavor of the Chipotle pepper through the smoke, but it all depends on how much you apply. You could also substitute Ancho chili which won't give you any heat, but it has a good earthy, sweet flavor.
1/4 cup sugar
1/4 cup packed brown sugar
1/4 cup kosher salt
1 tablespoon Hungarian paprika
1 tablespoon chipotle pepper
1 teaspoon cayenne pepper
1 teaspoon freshly ground black pepper
1 teaspoon ground cumin
1 teaspoon garlic powder
1 teaspoon Accent (MSG)
Before applying the rub, I first apply a light amount of yellow mustard and let the ribs stand for a couple of hours.