Melt butter in a large skillet over medium heat. Once melted, brush a 9 x 11 baking dish with some of the butter and add sliced onions to the skillet with the remaining butter. Cook the onions over medium heat for about 10 minutes until edges begin to brown. Add the garlic and thyme; cook 2 more minutes until fragrant.
Stir in the cream, potatoes, squash, cauliflower, salt and pepper, with the onions and bring to a simmer until the vegetables are barely fork tender, 10 to 12 minutes. (A little chicken broth can be used to thin the sauce, if needed.) While the vegetables are cooking, make the shallot crumb topping.
FOR THE CRUMB TOPPING:
Saute the shallots in a skillet with the oil over medium heat, stirring occasionally, until golden in color, about 10 minutes. Remove from the skillet and allow to cool slightly. Toss with the panko crumbs in the same skillet to combine; sprinkle over the top just before baking.
LAYERING THE DISH:
Ladle 1/3 of the vegetables with some of the sauce to the prepared baking dish forming an even layer on the bottom. Layer 1/3 of the ham on top of the vegetables and top with 1/3 of the cheese. Continue layering the vegetables, ham, and cheese, ending with a layer of the cheese for the top. Sprinkle with fresh parsley and the shallot-crumb topping; bake until golden brown and bubbly, about 30 minutes.
Remove from the oven and let sit for 10 minutes before serving.
Substitute the vegetables in this dish for your favorite vegetables (SEE veggie recommendations earlier in the post).
Use sliced or cubed ham.
Substitute smoked turkey for the ham.
Sweet shallots are perfect for flavoring the crumb topping. If you cannot find shallots use red onion instead.
Make it gluten-free—Use gluten-free breadcrumbs for the crispy crumb topping.
How to Make Ahead:
Prepping and freezing meals ahead is a cooking method I teach in our Monthly Cooking Online Course. This is how we recommend prepping this scalloped vegetable and ham dinner to bake and serve at a later time.
Prepared this dish right up to the point of adding the crumb topping. Cover and refrigerate for up to 3 days or freeze for up to 3 months (defrost before baking).
When ready to cook, heat the oven to 375°F and bake the casserole for 40-45 minutes until the sauce is hot and bubbly. NOTE: If the casserole is in a glass baking dish place it in a cold oven and set the temperature to 375°F. Cook for 55-60 minutes, or until bubbly and browned on top.
Add the crumb topping the last 20 minutes of baking time.