I agree. Following along these lines, ME2 actually has nothing to do with stopping the Reapers. We waste time trying to destroy the remnants of the Collectors, who have only one ship, destroy an entire Batarian system to delay the invasion by only 6 months, work with a terrorist organization ruining Shepard's reputation and making Council even more weary to take steps against the Reapers based solely on Shepard's words, act as a Spectre in the Terminus systems creating more tension between the Terminus and the Council...
To be fair, though, we don't actually know the... shall way say, insignificance of the collector threat until the ending. Pretty much up until that point we were under the assumption that the collector HOMEWORLD was beyond the omega relay. All we really knew for certain as that this race (collectors) were highly advanced, working with/for the reapers, had a keen interest in humans and human colonies and they come from the omega 4 relay. Was anyone really expecting the collector homeworld to turn out to be just a giant collector ship?
Though, in hindsight, one does have to wonder how exactly Shepard planned to stop them if they actually DID have a homeworld on the other side. Say, a homeworld that was essentially a massive industrial manufacturing hub preparing for war due to the incoming reaper invasion. How was one squad and one ship suppose to stop an entire planet? Its a good thing the collectors were such a relatively minor opposition consisting of just one giant ship that you could conveniently blow up with a single portable explosive. It's reasons like this, imo, that its best not to think too heavily on fictional stories.
All that aside however isn't it really the reaper connection that draws Shepard into the whole thing in the first place? Sure, saving human colonies plays a role, to be sure, but the 'selling point' that got Shepard to agree to work with Cerberus was that they (collectors) were connected with the reapers. If Shep wants to hinder the reapers what else could he/she have done at that point? It's not like anyone was really listening or taking the threat seriously. Action is better than inaction and Shep did, in the very least, throw a wrench in the reapers plans - even if its just an ant gnawing at the heels of a giant.
Like I said earlier, indoctrination is not an all-or-nothing event. There are gradations of it. The more willpower a slave has, the more useful they are - and indeed, the truly insidious power of weaker indoctrination is by having the indoctrinated individual carry out a plan that they THINK is their own, and do it fully willing, while in reality it works towards the Reaper's goals.
Initially, all the Reapers wanted was Shep's body for study after he died. Just as Saren was allowed to construct a facility to study the effects of indoctrination, so too was TIM allowed to carry out the Lazarus Project and revive Shepard. The Reapers obviously would not want Shep to once again be gallivanting across the galaxy kicking their ass and laying alien babes, but the alternative - forcing TIM not to do it - would be counterproductive to the insidious nature of their indoctrination. As pointed out in ME1 like forty times, the more the Reapers exert their influence, the less useful the slave becomes.
And so, TIM revived Shepard and attempted to destroy the Collectors because to him, he really was looking out for humanity's best interest. What followed in ME2, and continued into ME3, were a series of events that not so coincidentally were directly beneficial for the Reapers.
So yeah, his indoctrination isn't even really debatable. It's a thoroughly obvious plot point. In ME2, the implications are much more subtle, but clear in retrospect and especially with evidence from other out-game canon sources. In ME3, they literally beat you over the head with it, to paraphrase: "you're clearly indoctrinated (on Mars)", "Cerberus is working with the Reapers" (like ten different characters say this throughout the story), "was Udina indoctrinated, like Cerberus?" (the Coup), "I thought Cerberus was working with the Reapers?" (Horizon).
And yet, people still completely and totally miss this, and think TIM wasn't indoctrinated until he implanted himself with Reaper tech near the end of ME3. Lol, no. Like Saren before him, that was just the coup de grace. TIM was totally fucked long before that.
I agree that TIM was indoctrinated before the implants however I don't agree with you on when it occurred. Not that you don't make a lot of interesting and good points and observations but it still doesn't fit well, imo, with TIM or Cerberus. Even assuming what you propose is true, that the collectors had control of TIM from the start and just didn't stop him from resurrecting Shepard or actively working against them because they didn't want to rush the indoctrination (which I'm not against, in of itself, mind you)... theres still no reason they should had lost Shepard's body to Cerberus.
Harbinger, through a collector, was working with the Shadow Broker to obtain Shepard's corpse. Cerberus swiped it out from under them. Harbinger was pissed. I can understand them not risking their long-term indoctrination plan by taking control of TIM that early but if he was indoctrinated wouldn't they KNOW his plans? They wouldn't have to make him stop, they could just plan accordingly and be one step ahead of him. They could had warned the Shadow Broker in advanced. There are many steps they could had taken to keep TIM from getting Shepard's body if he was indeed indoctrinated that wouldn't require them actually taking TIM over.
This actually applies throughout the entirety of the second game, really. Sure, they wouldn't stop TIM from sending the Normandy through the omega relay but they would know exactly when you're about to make the jump. They would had placed more security waiting for your arrive other than just a few space disco balls, right? If TIM was indoctrinated that early in the series, even if they didn't want to directly control him or risk their long-term indoctrination scheme they would still know what he had planned. They'd be able to plan for it, prepare. They could circumvent every action Cerberus takes against them, all without directly taking over TIM.
As for the arguments of TIM sending Shepard on board the collector ship trap and the dead reaper being support of his indoctrination at the time, well, personally I see this as all circumstantial. Unlike Shepard, I actually agreed with TIM's reasoning for sending them into the trap. Before thinking the possibility of a leak getting out being preposterous lets not forget that the Shadow Broker has live-cam feeds of the Normandy security cameras. The normandy is not as secure and private as one might think. When TIM said that telling Shepard could had tipped the collectors off in any number of ways, I feel that is justified and reasonable.
The dead reaper ship is a bit different. It's important to remember, I believe, that TIM didn't JUST send Shepard out to the ship. He sent a team to investigate it after it went quiet, they just didn't make it. We needed that IFF and attempts of retrieval had failed.
Plus having TIM be this hidden Indoctrinated Agent from the very start would had to be a bit more planned out, imo. Cerberus and TIM weren't even planned up until the start of ME2. I can't help but feel skeptical of there being that deep of an important connection underlying the whole thing that far back when they didn't even come up with the character until the halfway point of the trilogy. Though I admit this bit is just as circumstantial as the collector trap argument and doesn't actually mean anything definitive. Just my personal feelings on the matter.
I completely agree on your stance regarding the novels and your OT remarks about Cerberus' infiltration of the citadel, though.