Okay... Since I'm as big a fanboy of the series as Yahtzee is of Silent Hill 2 and Prince of Persia: Sands of Time, I'm going to jump in and answer what my theories are in response to some of these. A lot of these theories came from TVTropes, especially in regard to the human reaper, so bare with me. I'll only address the latter two of the issues, since I admit you've got me there with the whole Omega 4 Relay thing.
The Human Reaper:
Okay, first of all, we didn't see any organic parts of Sovereign. However, we hardly saw the intimate details of that and the derelict Reaper you visit in ME2. Given the size difference between the Human Reaper and Sovereign, I think it's reasonable to assume that what we saw was the core. EDI does say that it would likely take millions more humans to fully 'grow' that Reaper to maturity, presumably gaining itself the squid-like shell of its kin. As for why they need one, since there's a lot of them, another theory I liked stated that the reapers aren't killing for the lulz, they're harvesting and recouping their losses.
The theory is that the Reapers are engaged in a massive war with some other species, and do a drive-by of the Milky Way every 50,000 years in order to gather resources and, ideally, grow more of themselves. If just half of today's human population was gathered and used to grow a reaper... Well, let's assume that one reaper takes, oh, 20,000,000 humans to grow. Given today's population of six BILLION, even if the Reapers only gather about 3/4 of the population, that calculates out to 225 shiny new Reapers. Probably not much compared to how many were seen in the end video, but that's still no small amount.
3. Accomplishments
Well, what we accomplished depends. When I was playing, I was under the assumption that ALL of the Collectors were located in that massive base, which was either blown up or cleared of all life for study. So, effectivly, we not only saved humanity from the Collectors, but Shepard and his/her team also eliminated all the Collectors, perminantly.
And in the process managed to spurn all the hibernating Reapers to wake up and enter the galaxy en mass, when it took an entire fleet to deal with one.
Whoops...