1. What is the main difference in portfolio management and prioritization between big companies and smaller-sized organizations?
The most obvious difference is that in big companies the portfolios are so large that no one person can get their arms around the potential opportunities and trade-offs between costs, ROIs and risks in the various options available for investing. In addition, there is usually intense competition for resources between the various assets.
2. How to be sure that the right projects are being performed? What are the key steps for successful prioritization?
"Right" is relative to the company's situation and objectives. The bottom line is that every company has finite resources, usually less than the ways they can invest those resources. If you can advance every compound you have, you generally will; if not, you want to invest your constrained resources in a way that maximizes your potential return. To do that, you need to estimate the costs associated with moving the compound forward, the probability of success for each step (or risk of failure), and the overall value of that asset, which is influenced by things like unmet medical need, size of the market, the competition, etc.
3. What are the main pitfalls that can occur in the process of prioritization?
I've already touched on some of them. Other risks are imprecision of methodology, differences in effectiveness of communication between teams, personal biases of the management team members, and going through a rigorous prioritization process and then doing everything any how.