Attorney General Martha Coakley is renegotiating a controversial settlement with Partners HealthCare after a state commission said Wednesday that a proposed takeover of two North Shore hospitals would raise costs and increase Partners' already formidable market power. Coakley's deal would allow Partners to acquire South Shore Hospital in Weymouth and Hallmark Health System in Medford and Melrose, while setting price caps and other limits on Partners' further expansion for several years. Coakley had structured the deal, announced in May, so that it could be revised based on findings of the Health Policy Commission, a watchdog agency.