If TIM is 100% himself throughout ME3, then that makes everything he does even worse, and it makes him a genocidal maniac. If he really was trying to pull off controlling the reapers in this way, he should have joined forces with everyone else and directed Cerberus to actively fight against the reapers, only to snatch control at the last minute.
TIM as he stands in ME3 right now is pretty terrible, as he's Indoctrinated, except when he's not (not to mention how he got Indoctrinated and where ME2 fits into all of that). And even then his Indoctrination logic is too small of a fig leaf to explain all his actions. In his acting he would be playing out some other Indoctrinated goal that would make his actions, like invading everywhere, more coherent; although all his conversations would have to be changed as well, perhaps he would only tell Shepard of his plan earlier if Shepard had more of a rapport with him.
His rational for not joining the Council and/or the Alliance was because he knew they would not stand for the experiments on Sanctuary; and that by moving out into the open he would have too many watchful eyes to try a last minute fast one. The explanation for attacking everything would be to play the part that he was Indoctrinated so he could continue to get his hands on the Reaper tech needed to retrace the signal to get the Control option to work. So basically he couldn't join the organics because they wouldn't trust him and he needed to be chummy with the Reapers so they would continue to lend him research materials.
I think it would be better conclusion to his character than Indoctrination induced Stupid Evil, replacing it instead with ruthless pragmatism. Plus it would help the ending by not having every option presented by the Catalyst. Personally, I think it also would have better delivered on all the build up every post Cerberus conversation had about TIM having a plan, instead of just being Indoctrinated. It's not perfect. It is trading nonsense for nonsense. But I do think it is a slight improvement.