Places I've worked at added chopped tomatoes, chopped lettuce, sliced olive, sliced, sauteed mushrooms, etc. Of course, we were using huge 15" tortillas for these.
Personally, I usually just stick with the cheese and meat items. If you want a really interesting flavor, crumble a little queso fresco (Fresh Mexican-style Farmer's cheese) over the cheese you normally use. Remember queso fresco won't melt. It adds an interseting creamy/salty flavor.
Chipotles in Adobo might over-power the quesadilla. Go easy on that, or just dribble a little of the adobo sauce out of the can into the quesadilla. Or, you can make a salsa and add some Chipotle to the salsa.
Personally, I like to make a Salsa Verde (using tomatillos instead of tomatoes) for chicken or pork quesadillas. I'll dribble a little over the meat as I'm assembling the quesadilla, while it's cooking.
Peace, Love, and Vegetable Rights!
Eat Meat and Save the Plants!