It's a trap. You can't control the reapers because they already control you.
And you control them right back.
Collective. Intelligence.
As far as I see it (when I look at Control literally), its a situation where we have a collective intelligence that can make better sense of things and have more programmed 'care' for organics (+ other synthetics in the Milky Way, depending on choices made in trilogy), compared to an Intelligence that existed nearly totally separate from organics and was hamstrung by Leviathan programming.
Does that mean that he's still controlled? Yes. But not in the direct definition of indoctrination. Instead, Reapers still send their intelligence to ControlShep, and he still makes decisions on that. If becoming an embodiment of information (which will always be limited, compared to the info, say, Synthesisverse can gain) is being controlled, then sure he is.
TIM couldn't do this because he was already changed to be someone under a control signal of the Reapers to the point of altering his identity. Shepard was not, though we could argue that the TIM confrontation scene had this to the extent of forcing him to move his body - yet TIM's ability there appeared more to be a form of biotics.
As a free willed organic that acted, even when Renegade, as the actual savior of the galaxy (though he can view himself as just a leader or soldier, the galaxy still eventually puts all respect towards Shepard), Shepard was the perfect candidate to take the place of the Intelligence. He was not controlled, he resisted control, so his 'superior organic code' was the best to act as a... ahem.. 'sovereign' entity. A (depending on POV) 'copy' of Shepard that would not just amorally take the intelligence of the Reapers and badly thought through programming and act on that, but one who, in a synthetic way, 'cares' for the galaxy and its safety and well being.
Is it the same thing as Shepard, the human person? No. And the galaxy may be losing out on the person who made the galaxy succeed against the Reapers, and you can headcanon how that may be a bad thing in the future. But it is still A Shepard and by all literal appearances, it is working for the betterment of both organics and synthetics (or at least organics under a guidance of synthetics for now). There may be a concern that this path trends the galaxy towards taking on (even if regarded as a 'purified form of') 'Reaper Tech' instead of any other chaotic development or the advancement of synthesis, and we're seen many of the complications of that, but especially on the Paragon path of the trilogy, we've seen a few examples of how 'Reaper Tech' need not be an absolute evil, but even a boon, even as it is always with the risk of greater disasters than if we didn't pursue it at all. "Nothing Good Came Out of Reaper Tech" is not what ME3 Shepard strongly believes unless he sticks to Renegade opinions the whole time - it was more of a ME1-ME2 thing and default opinion of his. People can change their minds.
And Paragon Shepard can do that at the 11th hour, from "We're not ready (to take the Reapers to dominate the galaxy for 'humanity' and even take them beyond the threats of the galaxy)" to "It seems we are ready (to use the Reapers to protect not just humanity, but everyone still alive in the galaxy, and keep the Reapers as a reconstructive and creative force in the galaxy, not a danger and weapon). And I'm ready to risk it." Shepard wasn't the one who wants human supremacy at any point - he's at most, like in ME1, a human protectionist or whatever. Something that changes in ME2, and is gone in ME3.
/literalism
/butIstillhavecrazytheoriesthatitisallalieoratleastamanipulatedtruthandshepardwakesup