The Catalyst introducing itself as the Reaper's controlling intelligence conflicts quite a bit with Sovereign's claim from the first game that the Reapers had no controller but was a race of 'nations' united around a common goal.

Ass Pull: The reveal of Catalyst and, by extension, the Reapers' motivation was infamously criticized by numerous players for coming pretty much of out of nowhere and clashing with some of the pre-established lore.

Even in-universe Shepard spends the whole fight mocking him. The only danger are the enemies he summons, but Kai Leng poses so little danger that the player can just ignore him while they deal with the enemies. He barely attacks you and his attacks are weaker than the Phantoms he shares similarities to, while also lacking their One-Hit KO ability, so he's actually less dangerous than a normal Phantom.

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.If Shepard decides against going to the academy, the Cerberus kidnapping operation succeeds and the victims are subverted into working for the organization, like Jack if she survived the suicide mission. The Academy and nearby Elysium later fall to the Reapers. After the students are evacuated, Grissom Academy is abandoned. Shepard encounters Kahlee Sanders, who has barricaded herself in a security room, and goes on to rescue the station's remaining students. If the Commander decides to travel there, upon arrival Jeff 'Joker' Moreau uses the Normandy SR-2 to distract the Cerberus cruiser and fighters guarding the station while Shepard and the team board it. Specialist Traynor and EDI connect the signal to a similar one known to have been used by the Illusive Man to lure Commander Shepard to a Collector Cruiser. The attack goes unnoticed because Cerberus uses a turian military signal to broadcast that the station is being evacuated by turian ships. Unfortunately, the Academy is attacked by Cerberus forces seeking to capture the students. In 2186 during the Reaper invasion, though war would close most schools, fewer than twenty teachers and students stayed at Grissom Academy to train biotics and prototype technology for the Alliance.

Mass effect 3 grissom academy