Looks to me like the Reaper is simply in "Engage the nearest target" mode. It's also likely that with Normandy's defensive upgrades, the Reaper determined that it would take too long to bring the ship down (and it might not even succeed) allowing the smaller targets to get away.
As for the Thanix, I'm actually pretty sure most of the fleets do have Thanix cannons at this point. Just because a Thanix absolutely sodomized the Collector ship doesn't mean it can do the same against a Reaper.
As for how they got to Earth so soon, it was the VAST majority of the Reaper fleet heading towards Earth where as Palaven, for instance, only appears to have had a handful of Sovereign-class Reapers in orbit around it. That and it's very likely the Reapers didn't slowly push the human fleet back to earth, more likely they came out of the relay and just made a b-line straight for Earth. As seen at the end of the first game, a Sovereign-class Reaper can just plow straight through a dreadnaught as though it were made of paper machete. They probably came out of the relay and just kept going, shooting/running through things that were directly in their path but otherwise ignoring the human fleet.
One thing you have to keep in mind about the upgrades is cost. The codex description for the upgraded hull armor has diamond particles fused into it making it ridiculously expensive. The Cyclonic Shield Projector is a tradeoff. I forget the details but I recall that it was a lot better than standard shields at some types of enemy fire but it was never designed for sustained combat or something and collapses sooner than standard shields (or something like that).DVS BSTrD said:
As for the Thanix, I'm actually pretty sure most of the fleets do have Thanix cannons at this point. Just because a Thanix absolutely sodomized the Collector ship doesn't mean it can do the same against a Reaper.
As for how they got to Earth so soon, it was the VAST majority of the Reaper fleet heading towards Earth where as Palaven, for instance, only appears to have had a handful of Sovereign-class Reapers in orbit around it. That and it's very likely the Reapers didn't slowly push the human fleet back to earth, more likely they came out of the relay and just made a b-line straight for Earth. As seen at the end of the first game, a Sovereign-class Reaper can just plow straight through a dreadnaught as though it were made of paper machete. They probably came out of the relay and just kept going, shooting/running through things that were directly in their path but otherwise ignoring the human fleet.
There's still the matter of cost, my friend. Just because you have the technology doesn't mean you have the money to integrate said technology into every ship in your fleet. As I mentioned before, I believe in the War Assets codex it actually does mention that a lot of ships now rock out with a Thanix. And also as I mentioned, while the Thanix was proven to be the bane of the Collector ship, we really don't know how effective it is against a Sovereign-class Reaper whose technical specs can only be described as "Holy shit this thing is nigh indestructible." I mean hell, Sovereign himself had the remains of 2 fleets and the majority of a fresh fleet focus-firing on it and the only reason it died was because it's consciousness was currently inhabiting Saren's corpse and so when said corpse was destroyed, it stunned Sovereign just enough to lower its shields and open it to attack. At least that's what my interpretation of the ending of Mass Effect is. 
