So why should TIM, who's writers declare that his intelligence is his weapon, think that he'll have more luck controlling the Reapers when he couldn't even control the GETH? Again, the same synthetics that the Reapers themselves were able to control and manipulate with ease. His motivations are like a fourth grader who keeps failing his math classes and decides he's going to tackle integral calculus instead.
Why? Because he's indoctrinated of course.
It's clearer if you've read the 3rd book as it's partly from the POV of a character implanted with reaper tech (Cerberus's prototype for the troopers we saw in-game) and being slowly indoctrinated. Basically though, part of what they do is get the subject to convince/delude themselves into believing what they're doing/being compelled to do is right, or at least necessary.
It's not *total* control as some seem to think. That level of control is pretty aggressive and turns the subject into something as mindless as a husk. It's really more subtle and insidious. The drawback of course that with enough cognitive dissonance and willpower a subject can fight the process. There's no breaking free of it though once they have you since if it looks like you're no longer "co-operative" they'll just tighten their grip, even at the expense of diminished mental capacity. Hence why both Saren & TIM topped themselves in the brief moments they were able to wriggle free.
Indeed, in hindsight it looks like TIM's insistence on bringing back Shepard *exactly* how she was (which was always dubiously justified at best) may have been the Reapers' idea. *That* certainly make more sense and is consistent with Harbinger's fixation.