As someone who loved to join the Temple or the Cult in Morrowind, I've been missing religious factions in TES ever since. TESO will only have the Fighters and Mage guild at launch, and even after, only the Brotherhood and Thieves guild have been mentioned. So, I'm not holding my breath for any full-fledged religious faction.

However, what if we could circumvent the man- and mer-made religions and cults alltogether, and simply appease directly to the gods of our choice? Of course there'd have to be a lot, as there are hundreds of gods in Tamriel, but just having the Aedra and Daedra for now would be great.
The reputation system could work similarly to the Fighters and Mages guild, where you have to destroy dark anchors or collect books. I think there are a lot of possibilites to do such tasks for the gods, but I'm unsure what ZOS is willing to implement.
Maybe somebody has an interesting idea ("Crafting" cheese for Sheogorath? Collecting Werewolf skins for Hircine?)?

In any case, such a system could provide several benefits to the worshipper, like better blessings, the access to specific craftable items, or even new abilities to use in combat. Possibly, artifacts could be tied into the system as well. And it is easily extendable both in width (more gods) and depth (more benefits).

I think it could be very interesting if there is a specific bonus for joining a group aside from a role playing prospective. Similarly to the different covenants in dark souls. This could, however, prove to be incredibly challenging to balance in a competitive game while still keeping it interesting.