Yes, those soldier's were husks. Shepard is not. TIM can not control people.
The point is, that his method of indoctrination was different from Reapers method. Since he installed Reaper tech into himself, his powers should also increase.
A) That's assuming the Reapers are trying to indoctrinate one another, or they can't help sending the indoctrination waves to each other.
As far as we know, Indoctrination requires only constant exposure to Reaper's tech. They're exposed to it all the time.
That said, we have no idea what "Higher mental functioning" is to such a mind. For all we know, the Reapers could be mentally retarded compared to their true potential. This would certainly be relevant if say, their controller (if indeed there is one) is using indoctrination on them.
They don't look like gibbering animals to me.
The rogue faction were the ones who thought they could control the Reapers! The equivalent of Cerberus in this cycle. *facepalm*
Guh.
Cerberus is wrong not because they want to control the Reapers. They're wrong because they're trying to sabotage the Crucible. If they wanted to control the Reapers and helped to build the crucible, they wouldn't be even villains.