Are you? I mean, there is nothing in the lore that supports your statement here. It is just a conclusion that you and many other fans have jumped to.
Dude, we literally see his eyes changing after he's hit by energy from the Monolith, a Reaper artifact.
Nothing before their arrival indicates that he was doing their bidding -- just about everything he did was counterproductive to their goals.
I didn't say they were controlling him during ME2. Actually you know what? He was probably influenced by them even back then. You know, him hearing voices and having visions of the Reapers is pretty weird.. sounds like subtle indoctrination. But anyways, I'm saying that during the 6 months between ME2 and ME3, the Reapers started using him.
Cerberus itself was set up with the purpose of fighting the Reapers, all of its working contributing to achieving those ends. Don't believe me? The manifesto makes an obvious allusion to the Reapers.
Absolutely not. The manifesto talks about aliens (not the Reapers) coming through the Charon Relay. Cerberus was created to protect humanity from aliens and ensure our place in the stars. I suggest you read up on the lore.
Hell, his actions through most of ME3 do not indicate indoctrination, either. If TIM's goal of controlling the Reapers was not feasible or somehow desirable (as lots of IT'ers comically believe) to them, they would not have responded to Sanctuary as they did.
Literally everything TIM does in ME3 isnt helping us, it's slowing us down. TIM thinks that he's in control, but he's not. He thinks he's saving us, but he's making us lose.
Also, Vendetta. We know he does not give away information to indoctrinated individuals. Where did we find him after Thessia? TIM's office.
Vendetta was hacked. Pay more attention to the game.
Funny that you bring him up. Remember what he says when Kai Leng enters the temple in Priority: Thessia? ''Indoctrinated presence detected.''
Kai Leng is indoctrinated, just like every other Cerberus troop and TIM.
Oh and by the way, what does TIM do after learning that the Citadel is the Catalyst? He alerts the Reapers. Wow that sure is gonna make us win the war! Thank you TIM! You're such a non-indoctrinated hero! 
Yes, he was indoctrinated ... toward the end of ME3. By then he had thought what he got from Sanctuary would grant him immunity from indoctrination when he implanted himself. He was wrong. Before he implanted himself, though, he was himself.
Just face it man, he was indoctrinated all along.