Meanwhile, jahitr, your comment traversed through Cisco routers, all of which use Tcl as their core internal scripting language, to make it to hacker news. Dead indeed.
Because German and Swiss states couldn't stand up to a larger force organized hierarchically is not proof that humans have _not_ evolved to work in small groups, it is only very poor empirical evidence that a larger force with better weapons can defeat a smaller, disorganized force.
As for why people seek freedom, I doubt most consciously think about it in those terms. You seem to think that individuals ponder about the pros and cons of going it alone or being part of a collective, but it just doesn't happen that way. When you're brought up in a culture that is already one way or the other, and that is all you know, you rarely choose because it's not even a question that enters your mind.
I'd suggest reading Beyond Civilization by Daniel Quinn.
I've thought about how we could structure a business in such a way that no team became too large, and all functioned relatively independently across the country or the globe. I called it a "federated" business, which had a Constitution at its core that served the same purpose as the Constitution of the United States: to hold together these "federated" business tribes as one company. Each tribe did whatever work they wanted -- they had to find the work and do it, but could always request assistance from other tribes in the company who had expertise in areas they might need to complete a job. Any individual or tribe would be free to leave at any time without any restrictions. The only purpose of the "federal" part of the business would be to manage office-type things like legal, payroll etc. and possibly maintain a core tool kit that could be used by all of the others in their work. I figured out how to map it to the current corporate structure: each tribe would form as its own LLC; the core federated part would be an LLC as well, but would not own the others. There would be an agreement signed between the "tribe" LLCs and the federal LLC, but as I said, any of the tribal LLCs could "secede" at any time, as long as they fulfilled any open obligations to other tribes' customers. Also, all bylaws would restrict any tribe and the federal part of the organization from going public, even if they seceded. That would be the one restriction. I would only be interested in this kind of business if it were for the long-term, and not with the goal of flipping or cashing out. Not sure it would work as advertised, but it sure would be a cool experiment.