T.I.M. knew about the Collectors and the Collector Base well before-hand. Not sure how he does (that remains a mystery to be solved). He knew the Collectors were targeting Humans, that they only had one ship or a few ships, and that they used a small space station. He also knew they were working for the Reapers. How exactly did he even come to suspect that?
I mean how else could the "Suicide Mission" have worked? We know the Normandy's stealth systems don't do anything against the Collectors. So sending the Normandy in for recon was never the purpose. So if T.I.M. was as clueless as he says why would he send just Shepard and a team of specialists? A team of specialists wouldn't do squat against an armada of Collector Ships or if there was a Collector Homeworld.
No, it seems pretty clear T.I.M. knew or made a very good guess that the Collectors only have one vessel and they operate from sort of space station. The only instance it becomes clear that a Space Station could be all the Collectors really have is when we learn they are located in the Galactic core which as Jacob notes is very volatile due to the number of stars and black-holes. (I also suspect T.I.M. used the Reaper IFF before and actually scouted out Collector Space with a series of Probes. He probably lost the IFF and the ability to replicate it when the Derelict Reaper crew got indoctrinated.)
T.I.M. not only lied to Shepard (and not for the first time either), but also used Shepard for his own purporses. If T.I.M. really wanted to stop the Collectors why didn't he give Shepard some sort of large ordance like a nuke to destroy their base outright? Oh that's right! He wanted the Collector Base intact all along. He wasn't interested in saving "Humanity" or saving the Colonists from further attacks. He just wanted the technology. I mean he basically setup Horizon. And there's the problem. Maybe T.I.M. thinks he's saving humanity or leading us to a better future or whatever, but at the same time he sure has no problem killing his own kind if it means he might get access to great power.
Also the game itself make it abundantly clear saving the Collector Base is taking a big risk. If you talk to your Squadmates right after the mission, each and everyone of them will question your judgement about keeping the base. So they must all be exceptionally close-minded, even Jacob and Miranda who are Cerberus operatives themselves.
Cerberus is not Shepard's friend or ally. Shepard is just one of the many assests T.I.M. has at his disposal. If Shepard no longer serves T.I.M. any use or Shepard becomes too great a liability he will get rid of him. T.I.M. did not bring Shepard back to destroy or stop the Reapers, he only brought Shepard back to
help in that endeavor
. The Normandy SR2 itself is just as instrumental in stopping the Reapers and is probably more important to T.I.M. then Shepard is. Look if you've seen
this game ending it's rather clear what T.I.M. values the most.
1) Collector Base
2) Normandy SR2
3) Shepard
Regardless of whether you save or destroy the Base
T.I.M. wants his stuff back. He's not exactly the sharing kind if you hadn't noticed and the only reason he gives Shepard so much leeway is to dupe Shepard into buying his act that
he wants to help. Apparently it also managed to fool some players as well. Say what you will about the plot, the writers sure have a knack for creating believable characters. Come ME3 The Illusive Man will likely be regarded as one of the better "bad guys" to be created in a video game series.