Set a large pot of water to boil for cooking the linguine. While waiting for the water to boil, heat 1 Tablespoon of oil in a large skillet over medium-high heat. Add sliced fennel, onions, and garlic and sauté until slightly softened, about 7 minutes. Season with salt and pepper and transfer to a bowl.

Salt the boiling pasta water and cook the linguine until just tender but still firm to bite, stirring occasionally. Drain, reserving 1/2 cup of the pasta cooking liquid.

While linguine cooks, add remaining 1 tablespoon oil to skillet. Add shrimp and scallops, sprinkle with salt, and pour in white wine. Braise seafood, covered, until just opaque in center and shrimp becomes pink, stirring occasionally, about 2 minutes. Using a slotted spoon, transfer seafood to the bowl with the fennel-onion mixture. Add tomatoes to the same skillet and sauté until heated through, about 1 minute. Then return the fennel-onion mixture and seafood to the skillet.

Place drained pasta in a large, heated serving bowl. Pour the fennel, seafood, tomatoes, and skillet juices on top of the pasta and sprinkle over the chopped fennel fronds and 3 Tablespoons of parsley. Toss to coat, adding reserved pasta cooking liquid by 1/4 cupfuls if dry.

Sprinkle with remaining chopped parsley, and serve with lemon wedges and red pepper flakes.