Android Lollipop/Marshmallow full granular control of system app permissions I'm shocked this question hasn't been asked. I want an app preferably, but doesn't have to be an app. I need a way to be able to control all permissions on android Lollipop/Marshmallow. If you say Appops or in Marshmallow 'its built in the GUI', thats not an answer to this question because I'm asking for ALL permissions, not just some of them.

If this is the wrong place to ask the question, please direct me to the right place.
You'll need root to be able to do anything like that (beyond what's built-in to android). 

Look up XPrivacy, a plugin for the XPosed framework. It can do a lot of privacy-specific control of permissions. 

Or check out Privacy Guard in CyanogenMod Roms. Requires an unlocked bootloader to flash custom roms.

Autostarts only requires root, and it can prevent apps from responding to certain events.

Android isn't currently capable of what you want it to do. These mods may help, but in the end, it just isn't designed for full user control. While much less walled-garden than iOS, it still locks things down for the end user in many places.