I've just spent the last 5 years working on a USAID-funded global project that addresses precisely this issue: the Capacity Project (www.capacityproject.org). You are right that this is a critical but immensely challenging area of aid. There are no simple solutions, and there are so many interdependencies and unforeseen consequences. My particular area of focus is HRIS. It is amazing how many ministries of health don't even know who is working for them or where, and how much difference just a little information can make. Please come check us out: http://www.capacityproject.org/hris/
I believe the US is behind most of the rest of the world when it comes to nantionally mandated maternity leave. I work for a nonprofit that provides maternal health services mostly in Africa. With the exception of a couple of countries, most of the countries where we work have more progressive maternal leave policies than we do! This is a question of valuing employers and business over all else in our culture, despite politicians' claims to support family values.
Thanks for this rundown. I shared it with some of my colleagues. It doesn't seem surprising, considering Microsoft's track record, that the Gates Foundation would not be open about its processes or numbers. But it is distressing to see yet another large foundation as an obstacle to doing development in a different (more effective?) way.