Yes, the procedures are negotiated between the unions and the employers. In the case of public-sector unions, the elected government is responsible for representing the public interest in the negotiations. The legislature can also pass laws directly mandating certain procedures, if they wish, since ultimately the whole union system operates within parameters specified by the labor laws.
Imo public opinion has to align against police misconduct for it to be dealt with. If the public is offended by misconduct not being punished, this provides both an incentive for elective officials to make sure that can be done, and to police unions to be pragmatic about which kinds of interests they wish to defend; it may not be in the members' collective interest to defend a few bad apples, especially if doing so greatly angers the public. Of course, it might be in their interest if the whole lot of them are bad apples...
My impression, though, is that the majority of Americans are hardly concerned about police misconduct, and generally support the police against complaints, which doesn't provide very fertile ground for anyone interested in pushing reforms. You can win an election by being tough on crime, but can you win an election by being tough on police misconduct?