Mince the cilantro leaves and place in a bowl. Using a microplane, grate the garlic on to the cilantro, followed by the lime zest. Toss together and set side.
Heat olive oil over medium heat in skillet. Add onions and let cook until onions begin to soften, 3-4 minutes. Next, stir in sweet potatoes and continue to cook for another 3-4 minutes.
In a mortar and pestle, combine the chipotle, adobo sauce, honey, and lime juice. Break apart the chipotle into small pieces (alternatively, you can cut up the chipotle.) Pour into the pan with the sweet potatoes and reduce the heat to medium-low.Cook until sweet potatoes have softened, 10-15 minutes.
When ready to make quesadillas, preheat grill or skillet over medium-low. Brush one side of the quesadilla with olive oil. Sprinkle with 1/2 to 1 ounce of cheese, followed by half the sweet potato mixture, a hefty sprinkle of the gremolata, and finish with 1/2 to 1 ounce of cheese. Place another quesadilla on top and brush with olive oil.
Place quesadilla in the skillet and cook on each side until crisp and cheese is melting, 3 to 4 minutes per side. Remove from heat and continue with remaining quesadilla.