Yes, but the problem was the plot tried to have it both ways. Cerberus was moving troops and equipment all over the place and performing large scale operations, but the rest of the galaxy couldn't figure out any leads. If they hadn't had a lucky break, they've have been toast. It broke my sense of disbelief to think that Cerberus was so damn good they could pull off all those stunts and not have Liara's info network have at least some idea where to look. Heck, the moment I heard about Sanctuary I knew it was going to be some dodgy, probably Cerberus thing. Why not go there immediately.
The other thing is I didn't like TIM being so obviously indoctrinated and clearly wrong from the get go. I think it would have been better for him to be there presenting another option, offering Renegade choices that wouldn't be bound to the same sorts of moral restrictions that the Alliance would be. I'm mainly disappointed they missed a trick or two incorporating previous player decisions into the mix. I thought the choice at the end of ME2 could have had a major impact, but instead it ended up being basically +/- 10 asset points.