Reading Brian S recent contribution (nifty nifty map!) I suddenly realized that, outside the daedric and heart based religions, there seem to be, not two, but three other "Aedric" religions. Of course, you have men worshiping Shor/Lorkhan, and Mer worshiping Anuiel, but I find myself recalling a third option: Wherever Akatosh is not prominent, Arkay is. What is the relationship between these three?

Akatosh is the god of time, a prerequisite to mortality. Lorkhan is the creator of mortality, itself. And Arkay is the god of the cycle of life and death... yet another god of mortality. But he clearly cannot be the same as Lorkhan, since the Nords venerated Shor, while hating and fearing Orkey.

Is there an actual tangle here? Is there any way to follow the threads and discover it is not, in fact, a tangle, but rather a beautifully complex weaving?

No, but when it comes to the grand-ordering-scheme-of-things the next best thing for the cycles of time, is the cycle of live and death.

You'll want to see Tu'Whacca though, his story covers what you described.