Place oven rack in the top third of the oven and preheat oven to 500°F.
In an 8-inch, cast-iron skillet over medium heat, sauté the onion with garlic in EVOO until soft and slightly caramelized. Add the chipotle purée, some salt and cilantro.
Spread the onions in an even layer across the bottom of the skillet, top with the grated cheese and place in oven for 20 minutes, until golden brown and bubbly.
Remove from oven and pour excess oil off the top. Sprinkle with queso fresco, toasted pumpkin seeds and a drizzle of honey, and serve with chips.