Saute beef. Add onions, garlic, Italian seasoning, balsamic vinegar, worcestorshire sauce, and red pepper flakes. Add salt and pepper.
Remove from heat and set aside. In separate medium bowl, combine cottage cheese, cream cheese, sour cream, scallions, green pepper and parmesan cheese. Spread half of the cooked pasta in bottom of casserole dish. Cover with cheese mixture. Add remaining spaghetti. Spread tomato and meat mixture over top.
This can be made ahead to this point and kept over night or frozen. Remove from fridge before baking. Bake 350 for 45 minutes.