Harmony it is!
There are actually two major links between the stories mentioned: all involve worlds that go through cycles (like Scadrial) and all involve a Chosen One, as you surmised.
There are also specific ones:
Wolf’s Rain (Don’t read this one Marukka! HUGE spoilers!)
Belgariad/Mallorean
WoT: Saidin and Saidar are obviously inspired by Taoism - as was the whole R&P thing. But in the end they are the ONE power, as Harmony joins R&P into one.
AC 1-3 I actually liked Desmond, but setting that aside… The entire premise of the games is using the knowledge of the past to save the present.
No Place Like Home tells the story of a person searching through multiple religions for truth and purpose - only to find it in the faith of his own people.