Char the peppers over an open gas burner for 10 to 12 minutes, turning occasionally. Alternatively, char the peppers under the broiler for 7 to 8 minutes, turning occasionally, with the oven door slightly ajar to allow steam to escape. Place the charred peppers in bowl and cover with plastic wrap. When cool, peel and seed the peppers and slice lengthwise.
Heat 1 tablespoon extra-virgin olive oil in a medium skillet over medium-high heat. Add the onions, fennel and garlic and season with salt and pepper. Cook, stirring frequently, for 15 minutes, or until the vegetables are tender and sweet. Deglaze with vinegar and combine with the peppers.
Place a cooling rack over a baking sheet and place the chicken thighs on it. Drizzle the chicken thighs lightly with extra-virgin olive oil and season liberally with salt, pepper, and fennel pollen. Arrange rack in upper third of oven; chicken thighs should be 8-inches from the broiler. Broil the chicken thighs for 12 to 15 minutes, turning occasionally. Dress the cooked chicken with lemon zest and juice.
Arrange the chicken on a platter and top with the onions, fennel, and peppers. Scatter fennel fronds over the top.