It would be interesting if during the trial in the beginning of the game you could either spill your guts about Cerb and some of their deals and your actions which would get them kind of pissed. These choices could be a way to determine if Miranda for example will be friendly or join back with cerbs.
This also could be used to affect which ME2 party members who are possible companions to want to come back or kill you, or forget you.
As for why Cerbs wants you dead I'm assuming as mentioned in ME2 there are many different cells of cerbs out there....the ILM might be interested in making a deal or getting control of Reaper tech to remove aliens and leave only humans. After all ILM built Shepherd as he was 100 percent as a form of bait for the Collectors and Reapers. ILM could have trained an army but the one person who killed a Reaper is actually going to be of a threat.
All I know is i'm happy for no multiply and this going to be a fun ride to see the end to 3 part story.