Plus TIM seems to be looking beyond the war with the Reapers and how useful control of their technology would be to securing human dominance of the galaxy, so thats another reason controlling them probably appealed to him, heck thats probably the tract the Reapers used while indoctrinating him.
Does anybody remember the dead Reaper in Mass Effect 2? The one that was technically "dead"? That dead Reaper was able to indoctrinate all of the Ceberus scientists and turn them into husks. And TIM decides for no freaking reason that his next step should be to control the Reapers. No plan, no strategy, no anything. That's his plan and he's going for it. He's declared war on the whole galaxy to control something that is killing his science teams and soldiers in masse because... he wants to?
The Mass Effect artbook detailed TIM to be an endgame boss fight. It was scrapped because they wanted TIM's "intelligence" to be his weapon, not his strength. How the heck does TIM have Intelligence if he's indoctrinated and has stupid goals?