Anti-Climax Boss: The fights with Kai Leng are a joke, despite how much of a threat the story tries to pass him off as.

The Leviathan DLC clarifies a few things, by indicating that it's a limited AI doing what it was (badly) programmed to do, so its conclusions are not necessarily the best. A Broken Base has also emerged in regards to Synthesis, his preferred solution to the organic and synthetic conflict, and whether or not forcibly rewriting the DNA of every person in the galaxy would result in the utopian picture he and the Synthesis ending paints. Also his certainty concerning the inevitability of organic and synthetic conflict is called into question by Shepard possibly arranging a peace between the geth and the quarians. A lot of speculation ranges on just how well-intentioned and trustworthy he really is, which is fair since, being the leader of the Reapers, he's responsible for countless genocides.

There's a rather fair amount of this in regards to the Catalyst.

Incidentally, this would also bump Kai Leng down from The Dragon to The Brute. If he is indoctrinated, then he gets demoted from part of a Big Bad Ensemble with Harbinger and the Catalyst to being a Dragon with an Agenda or worse, the Evil Genius to the Catalyst's Big Bad and The Dragon to Harbinger. This causes some debate over how responsible he is for his own actions if he wasn't indoctrinated (or at least not enough that it could be called More Than Mind Control), then he did a running leap over the Moral Event Horizon a long time ago. The novels suggest he's been subtly indoctrinated for the last twenty years, where as he didn't get fully enhanced to Saren-levels until fairly late in the game. Most of it comes down to when he was indoctrinated.

The Illusive Man gets more of this in this game than he did in 2.

Mass effect happy ending mod