Preheat the oven to 400 degrees F. Halve the garlic crosswise to expose the cloves. Wrap the bottom half in foil and roast until very soft, about 20 minutes. Meanwhile, remove the skins from the top half and chop the garlic.
Heat 2 tablespoons olive oil in a large Dutch oven or pot over medium heat. Add the onion and sliced fennel and cook, stirring occasionally, about 3 minutes. Add the chopped garlic and red pepper flakes and cook, stirring, until the garlic softens, about 2 more minutes. Add the tomato paste and 1 teaspoon salt. Cook, stirring, until the vegetables are tender, about 3 more minutes. Add the tomatoes and 4 cups water; stir. Increase the heat to medium high and bring to a boil, then reduce the heat to medium low and simmer until the sauce thickens slightly, about 30 minutes.
Meanwhile, bring a large pot of salted water to a boil. Add the pasta and cook as the label directs. Drain, rinse under cold water and set aside.
Pulse the focaccia in a food processor to make coarse crumbs. Squeeze the roasted garlic from its skin and add to the food processor along with 1/4 cup each parmesan and parsley; pulse a few more times until combined. Set the breadcrumbs aside.
Lightly brush a 9-by-13-inch baking dish with olive oil. Add the pasta and sun-dried tomatoes to the sauce along with the fennel fronds, mozzarella, asiago and the remaining 1/4 cup each parmesan and parsley; toss. Transfer to the prepared baking dish. Top with spoonfuls of the ricotta and sprinkle with the breadcrumbs.
Cover the dish loosely with foil and bake 30 minutes. Uncover and continue baking until golden and bubbling, about 15 more minutes. Let rest 10 minutes before serving.
Make the pasta until the end of step 5, then cover the dish tightly with foil and freeze for up to 3 weeks. Bake at 425 degrees F from frozen, covered, 1 hour. Uncover and continue baking 25 to 30 more minutes.