Preheat the oven to 400 degree F. Line a baking sheet with parchment paper.
In a large bowl, combine the eggplant, tomatoes, garlic, 3 TBSP olive oil, salt, pepper and red pepper flakes. Spread the veggies on the baking sheet in an even layer. Roast in the oven until veggies are tender and the eggplant is golden about 35 minutes.
While the veggies are roasting, place the pine nuts in a small baking dish. Place in the oven on the rack below the veggies. Roast until golden about 4 minutes, stirring once. Remove from oven and cool.
Meanwhile cook pasta until al dente. Reserve 1 1/2 cups of the cooking liquid. Transfer pasta to a large bowl.
Transfer the roasted veggies to a food processor. Add the remaining 3 TBSP olive oil and pulse until the veggies are ppuréed, but not too smooth. It should still be chunky.
Transfer the puréed veggies to the bowl with the pasta. Add the Parmesan cheese. Stir to combine. Add the reserved cooking liquid 1/2 cup at a time until the pasta is saucy.