I always figured that TIM expected his research efforts at Sanctuary would give him the technology needed to control the reapers. I don't believe he knew (or suspected) that the Catalyst/Crucible enabled any options beyond destroying them.
It's odd - Saren also did some research into indoctrination - maybe the reapers would have tried to stop him, too, if they had been in-galaxy at the time.
Also, his motives for the Citadel coup attempt were never fully explained. Maybe he was trying to interfere with other galactic powers, or take control of the mass relay network.
Yeah, I guess so, he was looking for more conventional methods to control them. However, what Vazgen says is also plausible.
Funnily enough I just read up about Saren on the Indoctrination wiki, Sovereign used the implants he put into Saren to control him more efficiently, but only after Saren considered what Shepard said to him on Virmire about being indoctrinated. So maybe as long as an indoctrinated person doesn't realise there's indoctrination going on, the Reapers might not object to any research into this topic. But as soon as they start realising, them breaking free of the indoctrination is a too high risk.
True, forgot about those lines. An idea - he thinks that he can use the research at the Sanctuary in conjunction with the Catalyst to control the Reapers. But when on the Citadel, his vision changes. "The Crucible can control them. I know it can.", "I've dedicated my life to understanding the Reapers, and I know with certainty, the Crucible will allow me to control them". I guess that's when Reapers take full control.
Maybe the attack was aimed to destroy the research data? So the allied forces don't get the means to control Reaper troops. The ones conducting the experiments were not indoctrinated IIRC. Having a non-indoctrinated person to possess such knowledge is a risk.
Interesting ideas, could be
I guess TIM could have really gotten what he wanted from the VI already directly after Thessia. He broke through the VI's security protocols after all, didn't he?
Indoctrination is a cool and interesting topic, but for me also a bit of a tough one. Being so subtle, I never know how far it can actually reach, who is doing what why, or rather is someone still doing something of their own accord, or are they already too indoctrinated?
With TIM, it's especially tough. The comics show he's been indoctrinated for a very long time, but then it must be a very subtle, "light" indoctrination, I guess? We've seen what happened to other indoctrinated victims, like on the derelict Reaper. So there must be a bunch of different indoctrination levels, which makes it harder to see through this whole thing.