The Illusive Man knows ahead of time that the Collector ship is a trap, but he can't trust Shepard to not give away that he knows he's walking into a trap. His plan requires that Shepard blindly walk into a trap and escape anyway, which means his plan hinges on the gross incompetence of the enemy. Remember that in the mind of The Illusive Man, Shepard is the only hope for the galaxy. He'd rather risk the entire galaxy than suffer the chance that Shepard might ... do what? What was he afraid of that he was willing to risk everything? And if Shepard is too stupid to not give away that he knows this is a trap, then is he smart enough to get the job done at all? Well ...
Commander Shepard is an idiot for falling for this trap. The game never really gave you a goal except "Go on the ship. Okay, now fight your way back out." Why didn't he blow up the supposedly helpless ship? Why didn't he look for the bridge / engineering and try to take control of it? Why didn't he have explosives for wrecking the ship once he was inside? What was his goal? What was he planning on doing if there hadn't been a trap?
Later, The Illusive Man finds a derelict Reaper. (And in classic Cerberus style, he sent a bunch of scientists on board without ever checking up on them, leaving them to die hilariously in the name of Idiot Science.) He sends you on board to get the IFF. Remember that one of the great challenges that Shepard is facing is that nobody believes in the Reapers. So here we have one, all of a sudden. Then Shepard boards it and ... blows it up? How about taking a video and putting it up on YouTube, Shepard? How about offering tours?
Remember the whole point of getting the IFF is to go through the Omega-4 relay (Which no-on has ever survived!) and kill the Collectors. But, if our only goal is to kill them, then why go to all this trouble to pass through the dangerous relay and fight them on their home turf? Why not just sit on this side of the relay and spawn-camp them? Maybe put down some mines for good measure.
In fact, why not just blow up the relay? When the game came out, people suggested that Mass Relays were perhaps invincible. But then the Mass Effect 2 DLC came out and gave us a mission where you have to blow up a relay, retroactively making the entire plot of Mass Effect 2 a needless risk and a pointless waste of time.
At the end you're given a false binary choice: Blow up the collector base, or give it to Cerberus. If you blow up the base, then you really did come here for nothing. You're standing on a pile of technology, intel, and proof that the Reapers exist, but apparently it's "too dangerous", because ... I guess everyone else in the galaxy is too stupid to be trusted with it? But being forced to give it to Cerberus makes even less sense. The idea is that Cerberus is so strong they can take the base from you. But if they're powerful enough to overcome Shepard, who captains the most advanced ship in the galaxy, then they didn't need him in the first place. Why did they waste time bringing him back from the dead? This forms a nonsense Rock, Paper Scissors: Shepard Beats Collectors. Collectors beat Cerberus. Cerberus beats Shepard.