Why doesn't TIM tell you about preserving the Collector base before the suicide mission? Instead he forces the decision on you at the most dangerous moment. He doesn't give you time to think about the decision, or properly confer with more than two team members (if that matters to whomever), Anderson, the Council, or anyone else whom might be affected. Why would he want them involved? I can't imagine why, unless he really is acting out of the goodness of his heart, but clearly he doesn't want them knowing. That doesn't mean it's for necessarily bad reasons, but at the least, I'd call it selfish.
This is his history of "need to know" basis, and while I can see his justification, it's ridiculous to take him at face value. I start to distrust Anderson if he was giving the same missions and intel that TIM gave Shepard. I'd still trust him more, but that's because the two have a different history.
TIM has all the responsibility over his organization of Joe Nacchio. See previous Cerberus "rogue" failures, their invasion of the Flotilla, which Miranda has a nicer way of describing, and the directly hostile to Shepard Cerberus from ME1. What can TIM say to that? [I know you don't like my way of doing things]--or [that cell was rogue].
Is it unfair to TIM to distrust him because of his cliche appearance, lacking only a cat on his lap? Sure, it is. That's the direction given you by the game though. Opening scene, my thoughts were, "That girl looks like Mila Kunis," and "wow, is that Martin Sheen doing TIM's voice?" Immediately afterward, I got the distinct and obvious vibe that these people were manipulators, of the type commonly associated with conspiracy movies, some of them not to be taken seriously for how cliche they were.
It doesn't have to be logical to distrust TIM when the game clearly portrays him as it does. But then he tries to win Shepard's trust? Or does he? I actually have no idea if that was really his intent. He seemed to be dripping of ulterior motive from the start--holding a carrot on a stick for Shepard, because he knew she'd go after the Collectors/Reapers. Shepard also, as far as I'm concerned, was well aware of the risk, but was also aware of the fact that she'd be dead without Cerberus, at least as far as she knows. Falling in space with an air-leaking suit-->awake in a hospital-like environment: something went right. But nothing in the game ever confirms that Cerberus wasn't using Shepard, while there are plenty of reasons, yes some illogical like TIM's appearance to be suspicious.
I can understand the reasons for the lying about the Collector vessel, Horizon, and Freedom's Progress, or "not giving full info" as others like to call it. But as I stated before, his methods reek of dishonesty and manipulation. I realize the game tends to force the "big decisions" on you but even then you're more prepared for many of them (Legion at least tells you when you board the geth station, not while the decision is upon you) than TIM's final decision. To be frank, as the game went on I actually felt "maybe this guy (TIM) is okay, even though he's probably acting out of selfish desire more than he let's on." But then he pulls that, "oh, while you're on what's the most dangerous fight of your life, I'd like you do to this last favor for me, securing access to obscenely advanced tech which will further Cerberus's goals. It's for humanity, Shepard! Don't be stupid!" And to be honest, he convinced me and my first Shepard to preserve the base. But the more I thought about it, I wanted to blow that thing up on my "canon" run I'd be using for ME3. I can't say why other than that I don't like humanity playing the bully, which is exactly what I feared the outcome would be--TIM putting humanity not first, but atop the other species. The other more innate fear is that if humans pissed off the rest of the galaxy, they'd just band together and kill us all anyway. The Turians were in position to do it, but I guess it's safe to say that humanity was quickly catching up with the other species after joining the Citadel. At least that's the impression both games give you--not just ME2 with humans all over C-Sec, etc.