I watched the original Invisible Children movie in 2007 and I've kept up with their blog and story since, mostly at a distance. When we showed the movie at my high school back in the day people said all the same things they are saying now. The founders are getting rich off the organization, they don't audit their funds, they waste most of the money, they don't have a plan to end the war, the most is expropriated by dictators so I've looked into most of the criticisms before. This is what I know.
They have been audited independently since at least 2007. The two founders still with the organization make about $90,000 which less than Ophelia Dahl at Partners in Health makes. Most of the rest of the staff used to live pretty cheaply, sharing rooms in some houses IC acquired in San Diego and making, if I remember correctly, under $30,000 each. Whether they "waste" money is hard to answer. If I were running a charity I wouldn't spend as much money on education and videos as they do and would spend more on health. But I didn't go to USC Film School. I know that, despite claims to the contrary, none of their money goes to Museveni who anyone at IC will tell you kind of sucks and is no friend of the Acholi.
I think the best criticism of IC is that they don't have good answers on how to "end the war." They don't but I don't think anyone does. Look at this paper by Chris Blattman and his wife, who are supposed experts on the LRA, and you get he sense that like with most military interventions there are a lot of unknowns and anyone claiming otherwise is full of shit. That said I do think they have a coherent model. They believe that if you get people talking about Kony in the streets it will get people talking about Kony in D.C. and from that discussion some good policy will emerge. I don't see anything glaringly wrong with it.
It's sad some people always respond to IC with scorn and that most respond with temporary interest, but I like to focus on the positive. Tens of thousands of people have responded by spending at least ten hours of their time for this cause and that's great.