Add onions, celery, carrots, leeks, fennel, shallots, and garlic to a food processor. Pulse until everything is pretty finely chopped and mixed together.
In a large skillet, heat olive oil under medium high heat. Add thyme, rosemary, and sage. Stir constantly until fragrant, about 30 seconds. Stir in vegetable mixture and crushed red pepper. Cook until the vegetables are soft, about 15 minutes.
Stir in the wine and stir until almost evaporated, about 2-3 minutes. Turn off heat and cool to room temperature.
Meanwhile, stir breadcrumbs and milk together in large bowl. Add in beef and mix well.
Preheat oven to 450 F. Add cooled vegetable mixture to beef, along with eggs, Parmesan, parsley, ketchup, and Worcestershire sauce. Mix until well combined. Roll mixture into large (or small) meatballs to your liking.
Place meatballs on greased baking sheet and bake until cooked through, about 30 minutes.
Add meatballs to already made marinara and simmer for about 15 minutes.
Bring a large pot of water to a boil and add spaghetti. Cook until al dente according to package directions. Drain.
Serve meatballs and marinara atop spaghetti and with a nice crusty bread.