Heat the oven to 425 degrees. Toss the acorn squash cubes with 2 tablespoons olive oil, minced garlic, salt, and pepper on a baking sheet. Roast for 25 minutes until the edges turn golden and the squash softens.
While the squash roasts, bring a large pot of salted water to a boil. Cook the gnocchi according to package directions until they float, then drain and set aside.
Lower the oven temperature to 400 degrees. In a large bowl, combine the cooked gnocchi with the roasted squash and half of the shredded Fontina. Stir gently to mix.
Transfer the mixture to a greased 9-by-13-inch baking dish. Sprinkle the remaining Fontina evenly over the top.
Stir the panko breadcrumbs with the melted butter and remaining tablespoon of olive oil in a small bowl. Scatter this mixture over the cheese.
Bake for 15 to 20 minutes until the cheese bubbles and the breadcrumbs turn golden brown. Let the dish rest for 5 minutes before serving.