Heat oven to 400?. Trim the ends from the squash, then halve lengthwise, discarding the seeds. Transfer the squash, cut side up to a rimmed baking sheet lined with parchment or foil. Season with the salt and pepper and top with the shallots, honey, thyme and butter. Cover the squash with foil. Roast until softened, 45 to 60 minutes. Unvocer and set aside until cool enough to handle. Working in batches, scoop some of the softened squash and shallot from the peels into a food processor. Puree the squash mixture until smooth. Transfer to a serving bowl. Repeat with the remaining squash and shallots. Serve warm. Can be made and refrigerated for up to 2 days ahead.