My Theory: There are two factions of "Reapers"
1) Sovereign's Reapers who want to exterminate organic life.
2) Harbinger's Reapers who are trying to build their numbers and defeat the Sovie Reapers.
So yeah, basically i believe that there are original or "true" reapers which are Sovie type Reapers, who are trying to either destroy all organic life (or since that's impossible, keep it "down"). I also believe that some time ago, some species found a way to "Reaperize" themselves, seeing as how it was the only way to destroy the Sovie Reapers.
I assume that the original Reaper-Resistance Reaper was Harbinger, or his species. Since his (Harby's) creation he chose the most powerful species of the time, and ascended them into "Reaperhood". Most likely before Sovie type Reapers invaded through the Citadel Relay and killed off all other species.
To me, this explains why any species who was "Reaperized" would go along with it. (ex: i always doubted that say, a human based Reaper would go along with galactic genocide.)
I also believe that the Protheans were not enslaved, but chose to become implanted with Reaper technology so they could assist the resistance by helping Harbinger. I believe that the hologram of Harby in the end of the suicide mission was not so that Harby could control the Collector General, but so that the C.G. could communicate with Harbinger. Also, that Harbinger was not controlling the C.G., but that he was of free will.
Now, if my theory is correct, Harbinger's final monologue was aimed at both Shepard and the C.G. In that he told the C.G. that he has failed, but that the Harby Reapers would find another way to help their cause. Like, "Don't worry, we haven't lost yet", or something. But also that Shepard now has the attention of the Sovie Reapers. Like, "Good job genius, you're pretty screwed already but now you screwed yourself even more."
Also, my theory kinda makes sense because:
You go through the Omega 4 relay with a Reaper IFF, but still get attacked. Which now would make sense since you have the IFF of a "Hostile Reaper..."
The Omega 4 relay, the only Harby one (maybe) is the only one that is a different color than the others.
The view of the Reapers (Harby's) at the end of Mass Effect 2, does not show the Milky Way, but a different galaxy. I think it's once close to or within the Milky Way ( i might be wrong), possibly where the Harby Reapers are in hiding.
The Reapers destroying, not harvesting the Earth in the Mass Effect 3 trailer all look exactly like Sovereign type Reapers.
*Spoiler* Apparently, in Mass Effect: Evolution #2, the Illusive Man was implanted with Sovie Reaper tech. Which could mean his mission of destroying the Collectors was so he could destroy the Sovie Reapers Resistance. Which would also explain why the Harby Reapers begin their trek to the galaxy. Their option of creating more Reapers for their cause is over, and they have to act.
This is all just a crazy theory i came up with but i like it. All just my opinion also. Enjoy.