Whether or not you can negotiate the terms and conditions of your franchise agreement depends solely on the franchisor. Most large, well-known franchise companies will not allow changes to their contracts for two simple reasons: they usually have a history of successful and happy franchisees, and they know there are plenty of potential franchisees who would like to buy into their system.
Some states will not allow you to sign a contract that differs from the one they have on file for
You may find that some franchisors, even the big ones, are flexible in certain areas, like territory assignments, signage, and training. Newer franchisors are more willing to negotiate in many cases, including the initial franchise fee. If your contract is negotiable, contact as many existing franchisees as possible and ask them what deal they got so that you do not end up paying more.