Arrange fish in single layer in 13x9x2-inch glass baking dish. Mix lime juice, green onion, garlic, thyme, and chile in small bowl; season with salt and pepper. Spoon over fish; let stand at room temperature at least 20 minutes and up to 1 hour.
Heat oil in large nonstick skillet over medium-high heat. Sprinkle fish on both sides with salt and pepper, then flour. Working in batches, add fish to skillet and cook until golden and opaque in center, about 2 minutes per side. Transfer fish to paper towels to drain.
Cut off thin slice from each warm pita bread round, forming opening. Open pita pockets and stuff with fish, lettuce, and tomato. Serve with desired condiments.