Let me start by saying that this isn't based on any evidence, I suck at picking up clues. I hope you can think of evidence in favour of this theory or rip it apart. It is based on what I think the plot of the overall Cosmere story needs.
Every story needs a struggle, and as we have already seen struggles between Shards, we need something bigger. The only thing that comes to mind is Adonalsium and its opposing force, that has a weapon and is still around (as by WOB). So is Sanderson going to do a Raymond Feist and pull a bigger threat out of his hat? No, that is not his style, the struggle between Ruin and Preservation and Sazed taking up both of them was already forshadowed in the Heroes of Ages profecy at the very start of Mistborn. The bigger threat can only be Adonalsium or its opposing force, so we have to look at something or someone and a weapon that existed before Adonalsium was shattered, and that has some kind of presence throughout Sanderson's work. The only candidate we have left is Hoid as the opposing force and the First Gem as a weapon.
Now we only need to determine what Hoid wants. We have seen Hoid opposing Rayse and Ati, but what if this is not because they are meanies, but because they each shattered Shards? As we have seen Sazed demonstrate, it is possible to take multiple fractured Shards and put them together. Theoretically someone could reassamble Adonalsium by shattering all Shards and then becoming the Vessel for them. As he (according to this theory) hates Adonalsium, it stands to reason he wishes to prevent this. From Hoid's conversation with Dalinar in which he said he'd let Roshar burn if he thought that was the right thing to do, we can tell that protecting Roshar is not the reason Hoid opposes Rayse, so he must have an ulterior motive, and I think this is it.
Finally, you may wonder why I think Hoid is the villain and not the hero of this Cosmic struggle. I have two reasons:
1. Dramatic effect. Sanderson loves plot twists, the emperor of Mistborn and Hrathen from Elantris turned out to be good guys after all, maybe he'll pull something like this off again at a larger scale.
2. Hoid is a dangerous fanatic. When he said he'd let Roshar burn for what he thought was right, it immediately shifted Hoid from a fun cameo character to a much darker character for me. Considering to let multiple genocides happen is some crazy fanatic stuff.
