ME is a useful part of the system. It is in charge of watchdog timers (I think) and mid-level power management. The problem is that it is persistent and opaque. If the operating system were responsible for configuring and managing ME, it would allow it to perform these tasks without being so odious.
It also facilitates some hardware bring-up, and has management (hence the name) functionalities. So it's not really surprising that it has access to everything. That's not to say that it's at all acceptable that modern machines have such a gigantic security flaw.
