I'm somewhat skeptical of using real-life astronomy to determine where Humanity's colonies are. For one thing, I don't think that Bungie/Nylund put that much thought into their locations. For another thing, Halo takes place in an alternate universe anyway. Who knows if their stars share the same names as ours?

: If that's true
: then the Covenant could have went from the core worlds to Earth in about
: less than 5 days? It's a bit contrived I will admit, it's based on the
: record time from Reach to Earth after Reach fell, and the fact that Fred
: said that it would take the fastest Human ships at least 2 weeks to get
: from Earth to Onyx (And the assumption that Nylund was really paying
: attention to these details.)

As I said earlier, I think that last assumption is suspect. I'm more willing to treat the two weeks/five days figures as accurate... and even then, I think that the two weeks is factoring in ultra-advanced Human slipspace technology.

: Seems more likely that ships have always moved with the speed of plot.

"Moving at the speed of plot" is a phrase I borrowed from Michael Straczynski, when he was describing how fast the Starfuries move. Any vehicle in a story will move as fast as the plot dictates, but it shouldn't be so blatant.

It's also a problem with the games. A little editing in the cutscenes for both Halo 2 and Halo 3 could have gotten across the idea that slipspace transit isn't instantaneous.

: Although Covenant space seems to be a lot smaller than I thought it would
: have been as well, as of late. The Sangheili seem to regard Humanity's
: colonisation habits as being particularly notable amongst the other
: denizens of the galaxy and despise them for it due to its extent, which
: seems to imply to me that pre- war Humanity and the Sangheili are for some
: reason almost equivalent in territory. The UNSC should be ants to the
: Sangheili Empire, and the Sangheili shouldn't take notice of our little
: ant hole otherwise, should they?

If our respective territories are similar in size, how come the Covenant's territory encompasses the homeworlds of the Prophets, Elites, Grunts, Jackals, Drones, Brutes, and Hunters, while we're on our lonesome? Did the Librarian decide that Humanity needed Lebensraum?

: Their navy is also seemingly as
: dilapidated and as small as the UNSC's after Halo 3. Even after the
: Schism, a navy that has been built up and maintained for over 3000 years
: should be quite sizeable compared to the UNSC post Halo 3, and still
: easily capable of dealing with Humanity and the Infinity.

Actually, I think that we're supposed to think that the UNSC's fleet is larger. You don't hear the Humans worrying about the deplorable state of the navy.
The Covenant suffered some major losses in ships toward the end of the war from Cole's Last Maneuver, from Admiral Whitcomb's suicide run on the Unyeilding Heirophant and from the NOVA bomb. But High Charity's escort was the largest fleet that anybody had ever seen. I think the fact that the Covenant had that many capital ships in reserve speaks volumes as to the overall health of their navy.

As for dealing with the Infinity, I recall a short passage in First Strike detailing the absolutely comprehensive defenses around High Charity. Why wasn't the Sangheili homeworld similarly defended? Or defended at all?

: The disappearance of the Engineers is really strange. Maybe it's how they
: wanted to avoid Humanity becoming a Sangheili client race rather than
: getting anywhere near their "Reclaimer" destiny. That or it
: makes the Sangheili easier to mould into antagonists again due to the
: sheer desperation that it places them in. It seems like it must have a
: plot related purpose to it due to how erroneous it is.

Maybe Leviathan is right. 343i, and the writers they're hiring, have a real problem with "Because the author says so" creeping into the stories they create.