To prepare orzo, cook pasta according to package directions, omitting salt and fat; drain.
Place pasta in a bowl; stir in rind and next 4 ingredients (through 1/8 teaspoon black pepper). Toss to combine.
To prepare fish, combine fennel seeds, 1/4 teaspoon salt, and 1/8 teaspoon black pepper; stir well.
Sprinkle both sides of the fish with fennel seed mixture.
Heat 2 teaspoons oil in a large nonstick skillet over medium-high heat.
Add fish to pan; saut 5 minutes on each side or until fish flakes easily with a fork or until desired degree of doneness.
Transfer to a plate, and keep warm.
Heat remaining 2 teaspoons oil over medium-high heat.
Add onion and red pepper flakes to pan; saut 1 minute.
Add garlic; saut 15 seconds. Stir in tomatoes and capers; cook 2 minutes.
Remove from heat; stir in basil and remaining 1/4 teaspoon salt. Divide pasta evenly among each of 4 plates; top each with 1 fillet. Spoon 1/3 cup tomato mixture over each serving.