Preheat the oven to 350°F. Spritz an 9 x 9 deep dish baking dish or an 8 x 12 inch oblong dish with cooking spray.
Steam the sliced zucchini and yellow squash until fork tender, around 7-8 minutes. Drain and cool slightly.
In a heavy bottomed saucepan, cook the diced onion in 1/2 cup of butter.
Cook over medium high heat until soft, around 3 minutes. Add the Dijon mustard, all purpose flour, salt, pepper and garlic powder. Whisk over medium heat until combined.
Gradually add the milk, whisking constantly. Bring to a boil, then lower the heat and gently bubble for 5 minutes until thickened.
Add 1 cup of shredded cheese to the sauce and stir until melted.
To assemble: Layer half of the steamed squash into the bottom of the dish. Season lightly with salt and black pepper to your taste. Cover with 1/2 of the sauce and sprinkle with 1 cup of shredded cheese.
Repeat layers: Last layer of squash, salt & black pepper, remaining sauce, then ending with 1 cup of shredded cheese.
Melt 2 Tbsp of butter and toss with the cracker crumbs. Spread on top.
Bake for 35-40 minutes until golden and bubbly.