Preheat oven to 400 degrees. Toss butternut squash and fennel, each in separate bowls, with 1/2 teaspoon of the olive oil, season with salt and pepper. Roast on separate parchment lined baking sheets; 30 minutes for squash and 40 minutes for fennel, or until browned. Place in large bowl.
Heat 1 teaspoon of olive oil over medium heat in small pot. Add farro and thyme, stirring occasionally until almost translucent, about 5 minutes. Add water and bring to boil. Reduct to low simmer, cover, and continue to cook until liquid is absorbed, about twenty minutes.
While farro is cooking, whisk together remaining olive oil, dijon mustard, white wine vinegar, and sage. Set aside.
Combine cooked farro, squash, fennel, and cranberries. Toss with vinaigrette, serve warm or at room temperature.