Sounds like you did everything right and got just the right results. According to Cheryl Alters Jamison and Bill Jamison, authors of about 900 books on grilling, smoking, and barbecuing, the skin helps keep the bird stay moist but is sacrificed to the cooking process, as it absorbs too much smoke to be palatable. Let it go, they say.
If you really want to save the skin, however, Jamison and Jamison offer a pretty elaborate process in Book 864, Smoke & Spice (Canada, UK), that may give you the desired results. They inject the bird with a marinade the day before cooking (to improve the meat, not the skin), then rub a paste of garlic-flavored oil, mashed garlic, coarse black pepper, cayenne, and kosher salt inside and outside the bird and under the skin as far as possible without tearing it.
The next day, they dampen a 5-foot-long piece of cheesecloth and thoroughly wrap the bird and tie up the ends of the cloth. They moisten the cheesecloth every half hour for the first six hours that the bird cooks, then remove the cheesecloth (which must be one of the messiest processes in all of cooking-dom), and baste the bird with a favorite sauce every half hour until it is done (which they estimate will take 1-1/4 to 1-1/2 hours per pound in a smoker that’s between 200°F and 220°F).
It’s your call, but our money is on the skinless bird.