I worked with a large number of these so called "legitimate" charities and after what I saw I will never give a penny to any non-profit. You will have far, far more impact figuring out something you care about and directly spending $100 to accomplish that than giving $5000 to any of these organizations.
In what respect did you work with them? What is your main complaint? As far as I know, top GiveWell charities give malaria nets and stuff and it saves lives at fairly efficient rates.
Burkina Faso was one of Bill Gates biggest donation spots and it's had an endless series of unstable leaderships, insurgencies and coups in the last decade. This scares away both foreign investment and foreign aid. Countries like that have made lots of economic progress but seem to be stuck in this endless cycle of instability which is the bigger issue if the solution is to develop proper industry and proper modern housing sealed from insects.
Just because Bill Gates didn't solve all issues in Burkina Faso doesn't mean the donations were meaningless. Burkina Faso's GDP per capita has quadrupled since Bill Gates started donating, in addition to a lot of lifestyle indicators like child health and child mortality and so on. You certainly can't say his intervention made things worse.
