Heat 3 Tbsp olive oil in a large Dutch oven over medium-high heat. Add onion, carrot, and celery; sauté 10 minutes. Add garlic; reduce heat, and cook 5 minutes. Stir in tomato paste; cook 1 minute. Add wine; cook 5 minutes. Add tomatoes, basil, ¼ teaspoon salt, and crushed red pepper; simmer until reduced.
Heat 1 tablespoon oil in a large skillet over high heat. Sprinkle fillets with ¼ teaspoon salt and ¼ teaspoon black pepper. Add fillets, skin side down, to pan; cook 4 minutes. Turn and cook 3 minutes. Remove from pan. Add tomato sauce and 2 tablespoons oregano to pan. Add fillets, skin side up, to pan. Cover; cook 3 minutes.
Heat 2 tablespoons oil a skillet over high heat. Add squashes and bell pepper; cook 5 -7 minutes. Stir in remaining salt, remaining black pepper, remaining oregano and capers.
Plate fillets on top of sauce and squash mixture, top with sauce and fresh oregano leaves.