Heat olive oil in large skillet over medium heat. Add onions, salt and pepper and cook until caramelized, about 25 minutes.
Add eggplant and garlic and continue to cook for 5 minutes.
Add crushed tomatoes and red pepper flakes. Bring to a simmer.
While sauce is simmering cook pasta al dente according to package directions.
Drain pasta and add to tomato sauce.
Add burrata and basil. Toss to coat.
Remove from heat.
Sprinkle with parmesan and season to taste with salt and pepper.