Funnily, in an ironic way, Saren was the guy who cared about unifying everything. Look at his army. Geth, Krogan (with promises of cure), Asari, etc..
Then Shepard is almost (almost) railroaded to fill his shoes. Except it's "right" this time? Because why? Because it's nicer? I don't know..
Well, that kind of gets undermined by the fact that Saren was just a pitiful pawn in Sovereign's plot to retake the reaper trap, so all of his rambling about being subservient to the reapers was all for naught anyway. Even the geth were just following some silly machine worship to a being that was all idgaf, and the krogan were just clone drones that would undoubtedly be disposed of. We don't really get much in the way of any insight into Saren's whole idea about the krogan. We only get the idea that he intends to use them in the same way the Salarians did in the rachni wars.
It really didn't morph to that until ME3. Even ME2 was about finding lost human colonists and deciding whether Cerberus was worth working for...which is still a human centric concern.
Really, ME2 elevated the messianic qualities of Shepard, and it started right with Project Lazarus, which would be considered to be a wild farce if you really look at it. I mean, even Shepard can say that you could have trained an army with what TIM used to bring her back, but he invests tons and tons into resurrecting a single person. Sure, it pays off, but that's vidyagame logic right thar.
As for the story, sure it's about finding lost human colonists, but it's all based on the premise that humans are special because of their "genetic diversity" and are the singular focus of the reapers, to the point where they get some vorcha goons to distribute a virus that kills just about every alien except for them.
As for Cerberus, Mass Effect has never really been subtle about them. TIM might have been compelling and gotten a fair amount of support, but it was obvious that this guy was a villain in the making. I mean, he had the posh ass space station base overlooking a dying star and he had glowing eyes. Was anyone really truly surprised when Cerberus turned out to be an antagonist faction? Shepard couldn't say two words to TIM without sounding hostile, and everyone's constantly saying you couldn't trust them. Wonder of wonders that they all turned out to be right.