Prosecutors require police to bring them people to prosecute. If a prosecutor starts going after cops, they've now pissed off a group of people they rely on the get their job done, so most prosecutors won't prosecute cops.
I imagine this could be fixed by states having a special prosecutor specifically for those that are now considered protected by qualified immunity, which is more than just police. Also we should get rid of qualified immunity, which is an insult to the constitution.
On the criminal side I think prosecutors + police union negotiations for more lenient investigations are the big issue.