Yeah, the AI overlord of a billions of years old hyper-intelligence of a brainwashing, mind-controlling, indoctrinating, genocidal apex species is just going to step aside an let Shepard take over in his place. Because he's awesome and special.
Also because it has no ego to protect and will take a better solution even if it means its own destruction.
You are not the Catalyst. "You", that is Shepard, is killed. Vaporized.
Your thought-patterns are used to create a gestalt entity within the Reaper hive-mind which radically alters the entire Reaper state of being into something more friendly towards organics - basically giving the Reapers human morals, which was previously completley absent from their existence.
I've already died once and came back in a new form; I see no reason why I couldn't say that that happened again. It's a different form, to be sure, but while I have a new perspective, the base personality is still that of my Shepard, and I'll continue to roleplay it.
Foregoing the fact that you are brainwashing the Reapers to be a subservient slave species, Shepard is already affected by indoctrination. Any choice you make will be influenced by Reaper Indoctrination.
The Reapers were already a subservient slave species; all I'm doing is changing the boss, which is infinitely better than killing them outright. As for the indoctrination thing, this and the rest of the post is subjective interpretation. Enjoy it on your end, don't try to force it on mine.
As for ElSuperGecko: again, I'm the source of the indoctrination, and with my body disintegrated, I'll no longer be subject to it anyway in any conventional sense. When I've become the Catalyst, I'll control the Reapers utterly and my will will be my own for eternity, or at least as long as the Citadel stands. So I'm not worried about that. As for alarm bells, I'm sorry, but the guaranteed genocide of all synthetic life is a bigger one than any of the others. So, that combined with my previous post... sums up my response to that argument.