The Global Priorities Institute's research agenda is the best source I know of to find open research questions on cause prioritization.

The agenda is very long, and I'm not sure how often it gets updated, so I won't crosspost the whole thing here. But I do want people to be able to find the agenda by looking at tags, or searching for a keyword, which is why I published this. 

I'll post the table of contents as a preview for the full agenda: