Cut off about top one-third of apples. Remove cores and stuff with pecans. Season.
Add apples to roasting pan for last 30 minutes of cooking. Drizzle with maple syrup.
Combine cider, maple syrup, shallot, and thyme in a saucepan. Reduce by one-half. Make beurre manié by blending butter and flour in a bowl. Whisk into mixture. Continue cooking until sauce thickens. Season.
Cook parsnips in boiling salted water until tender. Drain and set aside.
In a skillet, caramelize onions in maple syrup and half of butter.
In a food processor, purée parsnips, caramelized onions, cooking liquid, and remaining butter until smooth. Season.
Let turkey stand for 15 minutes after removing from oven. Serve with baked apples, cider sauce, and parsnip and caramelized onion purée.