My predictions:
- At the end of ME1, the Reapers were all out in deep space save Sovereign who was the one tasked with opening the relay for them to come home. His destruction put a major kink in their plans and piqued their interest in Shepard and humanity since this probably had never happened before - or they would have left two reapers behind.
- Upon learning of Sovereign's demise the Reapers may have started a lengthy trip back to galactic space without the aid of the mass relay but I think it's more likely that they decided to wait and see if the mass relay was still a possibility. On a 50,000 year timescale, waiting two years for an attempt is nothing.
- Harbingers plan B was to use the collector and geth slaves to construct a human reaper. The human reaper was an experiment itself to see if humans would make good reapers, but it would have filled double duty by being tasked with suceeding where Sovereign failed. No downside to the Reapers here, only upside if it works and they get to shave years off their trip.
- Based on their interest in Shepard and the advanced tech required for the Lazarus Project, it's possible that they are somehow involved in Cerberus or with the Illusive Man. This seems a bit unlikely due to the actions of the Illusive Man, but it's possible that he is being manipulated and that the Reapers simply didn't value the Collectors very highly. They'll have a new slave race in the Geth once they get back to Galactic Space, so perhaps the Collectors had outlived their usefulness.
- Note that partly as a result of the actions of Cerberus, the council and the alliance are still largely unconcerned about the Reaper threat. In many cases you went on ahead while the official notice was delayed. The lack of alliance response to dead collectors could indicate that Cerberus sent cleanup teams around after you.
- After the collectors and human reaper were destroyed, the Reapers set out at full speed towards the galaxy. However, if the trip is only a matter of a few years then I have to wonder why they needed the Mass Relay in the first place. Appearing in the middle of the citadel is highly convenient for an attacking force, but if the journey is only a matter of a few years then it's negligible next to the 50,000 year cycle they operate on. I think it's more likely that they are hundreds or thousands of years away, after all the purpose of going away is to wait somewhere where they cannot be accidentally stumbled upon. As such, Mass Effect 3 will revolve around another plot to shorten the trip. I think this will involve capturing the Mass Relay perhaps involving Cerberus, and we may see a new group of Reaper slaves called into service along with possibly the geth being overwritten to all serve the Reapers.
- Also, the actions of the Prothean scientists seem to indicate that the Reaper fleet needs the Mass Relay to return. They returned to the Citadel after the Reapers wiped out civilization and modified the signal sent to the keepers so the Reapers could not employ the same strategy in the future. Yet they left no warnings about the Reapers behind at the Citadel, which indicates that they believed the threat was ended with the alteration of the signal. I guess it's also possible that they left a bunch of stuff behind but the Keepers cleaned it all up over the millenia.