Long ago, I made a mod somewhat similar to Wintersun. Would you like to adopt any of my ideas? :)

Hi Enai! Don't know if you know me; back in Oblivion, I made a few mods in a similar vein to yours. I never really found the time or drive to fully dive into it with Skyrim, but one of my better ventures (and the only one of any significance I updated for SE) was an overhaul of shrines and amulets. The SE version is of Divine Providence. (Glancing at it again right now, I may have overinflated some numbers, but that's not really what's interesting...)

You've done a FAR more thorough job with shrines than I ever thought of, but I did have one idea there you might find interesting: not all of my shrine blessings cure disease; about half grant a skill gain boost instead (in addition to their unique effect). Mara and Arkay are concerned with succor and comfort, life and death; but Zenithar wants you more productive! Expanding this idea to give other pantheons different thematic elements might be fun.

But it's my design around amulets that I'm really proud of. In addition to a basic effect when worn, they have a secondary effect which doesn't show up until you've had the amulet on for a day, and scales up as the amulet is continually worn (demonstrating devotion to that deity; kind of a parallel to your prayer system). Taking the amulet off resets devotion to zero, but the top tier of effects (which takes about two in-game weeks to achieve) is very powerful.

I don't expect I'll be doing any more updates, and Wintersun is hands down the better mod anyway. But if you're interested in taking any of this -- from the basic idea of doing something with amulets, to outright using my scripts (pretty sure I included sources, if not PM me) -- you have my blessing!