Only two things bugged me:
Sur'kesh. It's never made clear why Cerberus wanted to sabotage your efforts save for the hell of it, because it gives TIM more time to research his answer and even then, that theory is something the player has to infer themselves because the game doesn't say one way or the other. Curing the genophage and earning the cooperation of the krogan slows the Reaper advance and keeps Shepard busy, which helps TIM. So why do it in the first place? Same with the bomb on Tuchanka.
Also, the Coup, while an ingenious idea, had no clear endgame. Why did Udina agree to this? What did TIM offer him that made him change his mind? It was clear Shepard was making headway in convincing the other races to cooperate because by the end of Tuchanka you likely genuinely cured the genophage and secured Turian and Krogan cooperation, so why go to Cerberus in the first place? And what would Udina have done even if the Councilors had been killed? There's no way the other races would let him take sole power.