You make an excellent point, and unfortunately I only realized that after I had published this. Here's how I'd factor that in. The Illusive Man is on the Citadel. The way I'd see it, since the place is swarming with Reapers when you land into it, perhaps the Illusive Man is attempting to take control of them so he can secure the Catalyst, and he's succeeded, which is why they're fighting each other. This might seem a little Gears...ish but the idea that Shepard's appearance would have all of them converge on you would just make the gameplay more interesting. And I would allow Paragon Shepard to let him go and banish him forever...or Renegade Shepard to execute him where he stands. My guess would be that a lot of people would be more tempted to take the renegade option, but hey, it works.