Here are three, based on limited exposure to the organization (8 years, but obviously I didn't work in all departments/programs):
1. With such a large agency, sometimes information fails to flow down from the executive offices. There's an effort being made to get information about strategy and values and guiding principles to line staff and middle managers, but there's still work to be done.
2. There are advancement opportunities in headquarters, but the structure of some (especially smaller) regional offices and country programs makes it hard to advance. Some very bright, talented, hard-working people have had to leave the organization, because they didn't want to relocate but didn't want to stay in their jobs past a certain point.
3. In some units and departments, staffing capacity means that data analysis is not always as rigorous as it could be. With more quantitative people on board, the organization could look at the data it collects to see what is driving its outcomes. This would allow the organization to provide even better services to clients.