What do you do with a potential Federation member who is peaceful prosperous, the people are educated, well fed and happy yet they have no concept of democracy? Do you totally upend their culture to let them join or let them select their representatives by some other means? What if it's ritual combat to the death?
The body Kirk speaks of may just be the council. There may be a Federation assembly that we haven't seen yet. The council could handle the day to day stuff but the assembly could be where policy comes from. From what we saw in TBH the council chambers don'y look big enough to hold representatives from all the member planets and some of the seats were even taken up by non members (Dr Taylor, etc) There's even people in Starfleet uniforms there, wearing the same badge as the other, non-Starfleet members. Does Starfleet get a seat on the council? Perhaps when you join up you lose your voting rights on your home planet and gain some via Starfleet. This keeps Starfleet from being beholden to any one planet.