While many aspects of the franchise agreement are completely negotiable, franchise fees often are not. Federal law requires that franchisors notify all prospective franchisees of any material change given to any prospective franchisee. So if the franchisor negotiates a new franchise fee with one prospective franchisee, they have to then disclose that to all other prospective franchisees, which can cause delays and frustration in the negotiating process.
Although most franchisors will not negotiate on the franchise fee, that does not mean you cannot negotiate to get more bang-for-your-buck. An experienced and skillful franchise lawyer can often negotiate with the franchisor to get you larger territorial rights or more franchise training programs.