Great comparison, thanks for the insight Ben. Agree that Kiva and Garmeen are complementary, without Garmeen, there are less MFI to distribute the fund (more risk), and the fund can't be distributed efficiently. Here is another article on Grameen's model: http://indiamicrocredit.blogspot.com/2006/10/grameen-model-vs-self-help-groups.html
I think nonprofits like Kiva and Grameen are no different from tech startups. The sucess of Kiva and Grameen's Mifo project hinges on their long-term sustainbility, because much like VC money, grants and donations follow market trend, they come and go. If I were to compare the businese model of Kiva and Garmeen's Mifo, both tech projects. Kiva is an EBay and Garmeen is an Siebel. Garmeen will have a tough time building the MFI lending software and "selling"/deploying it to MFIs around the world. http://wiki.java.net/bin/view/Javatools/MIFOS
Once Mifo's feature set becomes mature, I think it makes more sense for Garmeen to go on a hosted model (eg. Salesforce.com), and opens up its API for MFIs to plug in customized functionalities.
Maybe one day Mifo will merge with Kiva?