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:

• Introduction
  • The Global Priorities Institute’s vision and mission
  • GPI’s research agenda
• 1. The longtermism paradigm
  • 1.1. Articulation and evaluation of longtermism
  • 1.2. The value of the future of humanity
  • 1.3. Reducing and mitigating catastrophic risk
  • 1.4. Other ways of leveraging the size of the future
  • 1.5. Intergenerational governance
  • 1.6. Economic growth, population growth and inequality
  • 1.7. Moral uncertainty for longtermists
  • 1.8. Forecasting the long-term future
• 2. General issues in global prioritisation
  • 2.1. Decision-theoretic issues
  • 2.2. Epistemological issues
  • 2.3. Optimal timing and discounting
  • 2.4. Diversification and hedging
  • 2.5. Distributions of cost-effectiveness
  • 2.6. Modelling altruism
  • 2.7. Altruistic coordination
  • 2.8. Institutions
• Appendix A. Research areas for future engagement
  • A.1. Animal welfare
  • A.2. The scope of welfare maximisation
• Appendix B. Closely related areas of existing academic research
  • B.1. Methodology of cost-benefit analysis and cost-effectiveness analysis
  • B.2. Multidimensional economic indices
  • B.3. Infinite ethics and intergenerational equity
  • B.4. Epistemology of disagreement
  • B.5. Demandingness
  • B.6. Population ethics
  • B.7. Risk aversion and ambiguity aversion
  • B.8. Moral uncertainty
  • B.9. Value of information
  • B.10. Harnessing and combining evidence
  • B.11. The psychology of altruistic decision-making
• Appendix C. Additional informal discussion