Cook spaghetti according to package directions, drain and keep warm.
Melt butter in large skillet over medium heat; add onion, cook 5 minutes, stirring occasionally. Stir in flour; cook 1 minute. Stir in milk, salt and pepper; cook 5 minutes, stirring constantly. Stir vegetables, scallops and shrimp into skillet mixture; simmer 10 minutes, stirring occasionally.
Remove skillet from heat; stir in cheese until melted. Divide spaghetti among four plates; spoon sauce over spaghetti.