Autonomy is a very strange Shard. They are placing avatars all over the place for seemingly no apparent reason. I was wondering what their plan could be, and I came up with a plausible theory.
There are two ways to become autonomous; you can either completely isolate yourself from outside influence, or you can bring everybody into your nation and all have the exact same view on everything. I think that Autonomy is trying to spread their influence throughout the Cosmere. They have also most likely aided Odium in splintering Dominion, another Shard that would like to conquer. Autonomy is currently trying to destroy Harmony through Trell, one of their avatars. They also have influence on First of the Sun (Patji), Obrodai (unknown Avatar), and Taldain (the Sand Lord). My theory is that in era 4 Mistborn, Odium will already have been dealt with, and Autonomy will be the villain. The Scadrians will have already dealt with Autonomy in era 3, and will know how bad they are. The plot of era 4 could be Scadrial recruiting the other two major Shardworlds, Roshar and Sel, and then they will clear out Autonomy in every planet.
Other crackpot theories about Autonomy are that Jaddeth, the god that the Shu-Dereth worship on Sel, is actually an avatar of Autonomy. This is how their priest is getting his visions, and the point is to convert all of Sel to Shu-Dereth so that they can worship Jaddeth/Autonomy.
Well, that's my crazy theory. Go ahead and completely tear it apart. I want to know what you guys think.