Lightly coat a 9×13-inch baking dish with nonstick cooking spray.
Cook the pasta according to the package directions until just al dente.
Drain the pasta and set aside.
Place the cottage cheese and ½ cup milk in a blender. Blend until smooth.
Melt the butter in a large saucepan over medium heat.
Add the flour and whisk with a wire whisk for about 1 minute.
Slowly add the remaining 1½ cups milk, whisking constantly.
Cook for 3 to 4 minutes, whisking frequently, until the mixture thickens slightly.
Stir in the blended cottage cheese, Dijon mustard, garlic powder, onion powder, smoked paprika, salt, and black pepper.
Reduce the heat to low.
Add 1½ cups cheddar cheese and the Parmesan cheese. Stir until melted and smooth.
Add the cooked pasta and stir until evenly coated with the cheese sauce.
Transfer the pasta mixture to the prepared baking dish.
Sprinkle the remaining ½ cup cheddar cheese evenly over the pasta.
In a small bowl, stir together the panko breadcrumbs, olive oil, and dried thyme.
Sprinkle the breadcrumb mixture evenly over the macaroni and cheese.
Bake for 20 to 25 minutes, until bubbling around the edges and lightly browned on top.
Let stand for 5 minutes before serving.
Notes
Tips and Tricks
Choose the Right Pasta – Elbows and cavatappi are great choices because their shapes hold onto the creamy cheese sauce.Check Your Protein Pasta – Some protein pastas soften faster than regular pasta. Keep an eye on the texture so it doesn't become mushy during baking.Shred Your Own Cheese – Freshly shredded cheddar usually melts more smoothly than packaged shredded cheese.Keep the Sauce Creamy – Reduced-fat cheese can become grainy when overheated. Use low heat when melting the cheese into the sauce.Make Ahead – Assemble the macaroni and cheese up to 24 hours ahead and refrigerate it covered. Keep the breadcrumb topping separate until baking. A cold casserole may need additional baking time to heat through.
Storing and Reheating
Refrigerating – Cool the macaroni and cheese promptly and store it in an airtight container in the refrigerator for up to 3 to 4 days.Freezing – Freeze individual portions in freezer-safe containers for up to 2 months for the best quality. The sauce may become slightly grainy after thawing.Reheating in the Oven – Place leftovers in an oven-safe dish, add a splash of milk, and cover with foil. Heat at 350°F until the center reaches 165°F.Reheating in the Microwave – Add a small splash of milk and cover loosely. Microwave in short intervals, stirring between each, until heated to 165°F.Thawing – Thaw frozen macaroni and cheese overnight in the refrigerator before reheating.