I go with the novelverse's approach - that ENT, TOS, TNG, DS9 and VOY are the same timeline. It's not perfect, but it's a lot simpler.
The novel Department of Temporal Investigations: Watching the Clock
does an epic job of tying every Trek time travel method into one complex but seeimingly coherent and consistent system. It also explains how and why some methods of time travel overwrite one history while others create an alternate branch.
Why is Enterprise classified as a New Earth series? Frankly, since Into Darkness has the only reference to Enterprise having ever taken place, I figured that it would be the only place to count this as canon.
What about the finale episode, which takes place between scenes of the TNG episode "The Pegasus"? Or the NX-01 crew records in the USS Defiant (originally from "The Tholian Web") in "In a Mirror, Darkly"? They're retroactive continuity, but they're pretty hard to ignore.
The universe presented in "In a Mirror Darkly" is different than the one presented in "Mirror, Mirror" and it's sequel DS9 episodes, namely, the existence of cloaking devices.
That was a big mistake in "The Emeror's New Cloak", since we'd previously seen MU Klingon and Cardassian ships decloaking in "Through the Looking Glass".