Preheat oven to 375ºF. Put pie crusts in pie tins if necessary and place them on a rimmed baking sheet.
In a large skillet, melt butter over medium-high heat. Add onions and cook, stirring occasionally until caramelized, about 6 minutes. Add zucchini and cook until zucchini is soft, about 6 minutes. Add red pepper and cook, stirring occasionally, until vegetables are wilted, about 4-6 minutes.
Add garlic and cook for 1 minute.
Turn off heat and stir in tomatoes, basil, and thyme and season lightly with salt and pepper. Set aside to let cool.
In a medium-sized bowl, beat eggs and half-and-half together. Add salt, pepper, grated gruyère, and crushed red pepper.
Divide vegetable mixture between two pie crusts, then pour egg mixture over each. Crumble goat cheese over tops. Bake for 45 minutes, or until set and cheese begins to brown on top. Remove from oven and cool for 30 minutes before serving.