You may be right about that, but there are different levels of alliance. Different political entitles can be mostly self-sufficient and still be politically united enough to work together in matters of common interest or share a common mission statement or set of core values.
True, but again, remember the immense scale we're talking about here. Hundreds of millions, if not billions, of different civilizations. There's just no way to keep track of all that at once, or to interact with all of them within a reasonable amount of time. Certainly, as I said, you could have networks of friendly relationships between adjacent civilizations, so one could be an ally of an ally of an ally of another civilization, and there could be enough cooperation that multiple allied civilizations could come together for a common goal as needed, but it would be piecemeal.
And it's hard enough even for the population of the United States to agree on a common mission statement or a common interpretation of its core values. When we're talking about quadrillions or quintillions of individuals in millions of civilizations, even nominal agreement on common goals is going to translate to a lot of disagreements and differences of interpretation in practice. Different groups will drift apart in their values and practices simply from the sheer infrequency of communication among them.
The perfectly mapped and replicated via hologram human brain down to the neuron may sound like insanity but not in Star Trek. A trillion processors working and storing information simultaneously about reaction, emotion, and so on sounds ludicrous but compare today's computers to the Moon Landings.
But as I said, most of the onscreen evidence shows that the Doctor can only be transferred rather than copied. Sure, you can argue in the abstract that something is plausible, but if the actual facts presented in the show depict a different scenario, then all we can do is accept that reality and try to explain it.
I'm not so certain as, basically, the same sort of thought has been shared with us on Earth. That a central world government is impossible because there's just too many people, too many different ideas, too many ethnic groups, and so on. However, even now, we live in a global community with representation.
Again: numbers. One planet versus billions of planets. It is simply a non-starter to propose that any Earthbound analogy could be informative when talking about a playing field billions of times larger. There comes a certain point where sheer numbers overwhelm everything else, where it would take centuries or millennia to interact even once with more than a minority of the other entities under consideration.
Theoretically, I could see it working like a pyramid.
Planet A is part of System B's government which is part of the Sector C government which is part of the Quadrant D government which is represented in the Federation. Indeed, if Slipstream ever becomes readily available, a central government would HAVE to exist to coordinate matters of interest across all these territories.
Why in the world would it
have to exist? That doesn't make any sense. In nature, many processes are regulated quite well by local rules. There's no central brain telling the molecules in a snowflake what overall pattern to form; they just connect at certain angles to the molecules immediately around them, and the operation of the local rules produces the emergent result of a higher order of structure. Same with an ant colony -- the queen isn't issuing orders to each individual ant, just churning out more ants that follow a limited set of local rules for interacting with their neighbors, rules which interact in such a way as to spontaneously produce higher orders of organization and complexity. Ditto for the neurons in our own brains, for that matter.
Besides, again we come down to raw numbers. Slipstream drive may allow travel to more distant worlds, but the actual
number of worlds that could be visited, settled, or allied with during the lifetime of a typical political entity or civilization would be finite. You'd still be settling/contacting the same number of worlds per year, they'd just be spread out a lot more widely. There just wouldn't be
time to contact and interact with every one of a hundred million civilizations in under a few millennia, no matter how fast your drives are.
There are simply too many of them.