User blog comment:Romig/Why Sovereign different than other reapers?/@comment-5093119-20130603204409

It is explained in the Codex that Sovereign was equipped with a flaw, the flaw which had him destroyed after he moved his conciousness to Saren's body during the battle of the Citadel. Because Shepard destroyed the new host, Sovereign's shields became weak and he began to fall, eventually being destroyed by the attacking fleets. So, I can conclude that under the assumption that Sovereign is older than most others of his variety, the energy was red because he was a different model of his form from all of the other similar models. Another guess would be that because the energy output is greater in an atmosphere (of a planet or the Citadel), perhaps it gives off a red colour.