Gentleman Moogle wrote...
Eh, I don't really put much stock on the Beacon as a reason. It's Prothean, and the Protheans -- assuming we believe the lore -- were all wiped out/assimilated by the Reapers. Anything the Beacon might mean to them, they probably already know from their buggified little slaves.
Besides, the Beacon was just a warning that the reapers were coming (I think. Haven't delved into the extended universe like some have), and contains no useful information on how to kill the darn things.
The Thorian... Not sure about that one either. It's dead now, and the reapers seem to be able to accomplish pretty much the same thing it did with their huskification/indoctrination process.
I'm still fairly certain that the whole thing revolves around Humanity's uniqueness as a species, and Shepard's as a person.
@Foehunter:
I have two problems: First; Collectors uplifted by the reapers? Aren't the collectors the Protheans, just genetically re-worked by the Reaps?
Second: I see nothing that suggests the "bird" was actually a reaper. there's not enough description there, and reapers are not known for their "studying" tactics. They're more the "Come, harvest, burn, leave" types. More than likely it was just your basic Prothean starship sent from the base on mars to study these primitive humans.
If there is Prothean DNA in Shepard though, it's going to be wildly degraded by this time. We're talking millenia since it would have been introduced into the genetic stream, and I just can't see it helping Shep right now.
I'm still going with "Humanity is unique". That there's just some quality about the species that is unlike that of others, and that interests the reapers enough to use us to make a new Reaper, and that Shepard is unique among humanity enough that the Reaps actually take the time to learn his name.
I was speaking purely from the perspective of what the Reapers might try to pass as "uplifted". After all, to help indoctrination work, the Reapers may have insisted that any genetic tinkering was for the Protheans' own good. Eventually, many of the Protheans would have cratered to the Reapers' demands. Look at Sovereign. It seems pretty clear to me that he convinced Saren that he would be spared, at least for a while, if he did as Sovereign demanded. That would have been quite the incentive to prevent any resistance to indoctrination on Saren's part. The Protheans were no doubt given a similar deal before their subsequent transformation into Collectors.
My argument about the wingless bird was probably premature. Although that red light from the bird before the caveman gets cut off seems to sound like the Reaper primary weapon.
I see your point about the Prothean DNA thing. My thought was purely from the standpoint that perhaps if the Protheans were monitoring, there had to be a reason. A potential reason would be because they were attempting to uplift humans, and they perhaps engineered humans with some Prothean DNA as a means to achieve that end. An alternative theory would be that the human uplifting was a fortunate side effect of Protheans using humans in Prothean cancer research.

If they did uplift humans, it would make no sense to use just one caveman for the job. In order for it to have any real potential effect, the genes would have to be introduced to a group of cavemen. It is true that the DNA would have degraded over time, and probably wouldn't amount to much by the time Shepard was born, but what if it was just enough for him to be able to handle brushes with Prothean technology without suffering serious injury. After all, Liara did say that a lesser mind would have been devastated by the beacon's surge of information.
All that said, what's the story on the Lazarus Project. What's up with those red glowing eyes and Husk-like scars for Renegade Shepard? That all definitely looks like Reaper tech.