User blog comment:The Milkman/What Happened to Harbinger?/@comment-101.165.126.116-20140409033824

The reason the illusive man becomes the main villan is simple. During the protheans cycle they had their own illusive men that cemented their destruction; splintering their worthy resistance into factions. Harbinger isn't just another reaper (hes a reaperfied Leviathan) and his significance in the war is diminished due to the fact that he cannot be reasoned with and because he is the "General" of the Reapers. Much like Hackett, he plays a vital role in the story by having an agenda rather then a direct impact. His personal interests in Shepard are what make him interesting.

Having the illusive man also served as a loregasm at the end. After the catalyst explains it's solution and you see that the illusive man was compassionate and brave enough to attempted to maintain the solution while saving (at least) humanity to prevent "The Chaos" from returning to the galaxy. It depicts the illusive man's decision as the paragon choice and Anderson's as the red. It shifts your expectations and makes it so much more of a significant ending.

The Leviathan DLC provides as much closure as possible for Harbinger and the Reapers themselves. Harbinger is a reaperfied Leviathan, the same way a husk is a reaperfied human. The rest of the Reapers are organ-synthetic copies, without the Leviathan traits. The interest for Harbinger can be sated by learning about the Leviathans because he is one. He's just... Less interesting... His motives are not his own either. They're the Catalysts. He's almost completely *just* a shell of a Leviathan which is why apparent from being interesting it isn't story line worthy