Use jack cheese in your cheese sauce and stir in a can of drained tomatoes or Ro-Tel (tomatoes and chiles) along with a bit of chili powder and cumin.
Stir in a cup or so of any cooked vegetable that your kids like. Cauliflower, peas, bell peppers, broccoli, green beans, etc, would all work well.
To up the protein, stir in cooked diced turkey or chicken, or add in a some drained canned tuna.
To change things up even more, vary the starch you use to make this. For example, you can substitute cooked white or brown rice, Israeli couscous, or even cooked barley or wheat berries for the pasta.