Okey, I am skipping all the rant about FSF not funding software projects to pay developers, or that the GNU brand is not "hot", but both feels a bit silly. The hotness of a brand is transient, and in reality, only a handful number of brands inspires users and developers. I can't see how GNU would be more or less hot than say Gnome, KDE, or apache which each has a large number of projects under them. As for funding, since when did any of those organizations actually fund the projects? They role is provide help in setting up funding systems, help with tax declarations and provide further legal help.
Thankfully, the last link in the end (http://lwn.net/SubscriberLink/529522/854aed3fb6398b79/) looks to bring some light of what the actually issues really are: copyright assignments being US only, who the "owner" of a community project is, Nikos' feeling that he aren't getting any tangible benefits from being under the name GNU, and last a request for more transparency in the GNU projects decision process.
As for those reasons, there are two I agree with and two I don't. Firstly, Copyright assignments being US only is bad and shows an inflexibility a non-profit foundation should not have. Their role is to help projects, and thus should be as flexible as possible and thus provide equal possibility to assign copyright to US or EU. Second, as for who the owner of a community project is, the answer should stare the developers in the face. It should always be the community (developers and users) that "own" the project and decides its fate. If Nikos' announcement had included a decision by the community (preferable in a transparent manner), it would had been hard for GNU to object. Third, Nikos' feeling that he aren't getting any tangible benefits from GNU are his to have, but legal assistance is something many projects value. If a project has no need for legal assistance, no need for help in creating donation systems, and don't feel a threat about lawsuits against individual developers, then a foundation such as GNU, Apache or other similar organization are not going to give much tangible benefits. Fourth, in regard to more transparency in the GNU projects decision process, I can only agree with Nikos. The corner pillar in a community is transparency, and GNU should be fully aware of this. If there are discontent growing because of an lack of transparency, it should be addressed and fixed with high priority.