ST has always played fast and loose with ranks. Again this is not really a big issue to me. Hardly indicative of bad script writing.
Oh it is. Would you buy that were it a film about the Navy? They make a point about how Starfleet is a military organization, and then they ignore it and make it look like that organization has no protocols whatsoever. That's bad.
It reduces the tiny bit of realism that is left in science fiction/space opera and makes everything extremely cartoonish. Same with the incoherent distances, and many other things.
Not really we already accept different ypes of warp drives, stargates, and other conceits to establish scifi universes, most of it is pretty far feteched in the first place, so the distance between warp and transwarp as a concept is negligible.
Nonsense, even in ST09 Starfleet isnt simply a military arm of the federation. Even if it were, every series has had questionable rank structure of some kind. Regardless, its a fictional series and not 100% analogous to the modern navy, its just used as a guide.