Bring a large pot of salted water to a boil and stir in macaroni. Cook, stirring occasionally, until pasta is al dente. Drain in a colander and shake well.
While pasta is cooking, melt butter in a large saucepan over medium heat, add onion and cook, stirring, until softened, about 6 minutes. Stir together milk and cornstarch in a large cup; whisk into pot with onion and cook, whisking, until boiling. Continue to cook, whisking, until thickened, about 2 minutes. Stir in peas and salt.
Add cooked pasta to sauce and stir well. Sprinkle Cheddar and Parmesan on top and toss well. Season with pepper to taste.
This turned out great. I used a mix of colby jack and reduced fat cheddar since that is what I had. I also reduced the milk to 2 1/4 cups since the picture looked a little soupy, and I thought that worked out great. I also used whole wheat mini shells. I will definitely make this one again.