I think the appeal of Mass Effect 2, to me, was always that when things have grown their most desperate, and truly despicable people have arrived to offer their help, Shepard does not have the luxury of refusing uncomfortable alliances.
We spent all of the first game hearing about how the Reapers are an existential threat to all life in the galaxy, that everyone must work as one to oppose them, that nothing matters more. The second game chooses to interrogate what the practical limitations of that stance actually are, or if there should even be any.
The player's new allies were ever present in the background of the previous game, kidnapping and assassinating people that you had come to know. Depending on player customization choices, they may have even had a role in shaping your avatar's personal tragic past. But they still heard the call when many refused it, have recalibrated their goals, and say they're willing to do their part to help. What should Shepard do with that? The game doesn't really have an answer, except for the obvious fact that you cannot progress if you refuse. But even so, it never really stops asking if you're really sure you're doing as you ought to be.
No member of the SR-2's new crew, save for maybe Kasumi, are people that Shepard would have spoken to without a gun the year before. A lesser story would have shied away from Mordin and Miranda's crimes, because the player is inclined to like them, or would have had unsavory politicians like Udina or the Quarian Admiralty disgrace themselves in some more obvious ways, that Shepard could be justified in removing them. Mass Effect 2 denies the player neat, tidy, satisfying answers to its moral quandaries.
The Illusive Man is a malevolent evil whose influence must be removed from the galaxy, and is also Shepard's strongest ally in the fight against the Reapers. Where is the line? Should Shepard and their team ignore Cerberus' nature, because they need them? Should we all say it doesn't really matter, because the STG and the Spectres are just as bad, and not think too hard about what Cerberus is doing when Shepard isn't watching them? Or should Shepard take the high road, walk away, and die?
To me, this is where Mass Effect was able to rise above it's roots as a Star Wars game with the numbers filed off, and become a world with emotional stakes.