User blog comment:ExSturminator01/Mass Effect 3 Predictions based on ME2 hints/@comment-323597-20100301165621

Rachni for sure, the news clips talking about ships mathing Rachni silhouettes is one thing but the message on Illium basically said that The Rachni are the enemies of the reapers, I think people who killed the Rachni queen will be unhappy when ME3 comes around.

Cerberus will either be an ally or an enemy in ME3 depending on if you save or destroy the collector base, there is also the possibility that your actions could end up upsetting the balance of power for TIM and you could see Cerberus "split" into two factions, one loyal to TIM and the other loyal to Shepard.

IMO if you save the collector base TIM will try to make a (relatively) small scale reaper-like craft, likely initially using cloned vat-grown biomatter but I suspect that as seems to be the case frequently with Cerberus the people who run the project will use people or aliens in order to produce results.

There is also the possibility of an incomplete or inoperative "prothean reaper" out there that could be a potential threat or maybe even ally. Maybe the "prothean reaper" worked but it was not loyal to the rest of the reapers because of the prothean connection, so the rest of the reapers imprisoned it somewhere.