I think being a Prime in the Aligned continuity is more than just being leader of the Autobots. If you read the novels it seems that Primacy has a mystical component to it as well. You have to be worthy of the title. So if Optimus were to be killed, Arcee wouldn't become Arcimus Prime or some such. She would just become the leader, if indeed she is the next in line. To become a Prime she would have to be chosen by Cyberton/Primus/whatever and be invested as such.