Thessia wasn't handled all that well, and the biggest reason it sort of failed wasn't even because of the fact that we got that ridiculous blinding spotlight and Kai Leng's immunity boosts, but rather that Shepard HAD the data within her grasp and the scene turned into an inopportune exposition dump when the best and obvious thing to do would be to snag the data and attempt to access its information in a safer environment.
This was a classic moment of Shepard carrying the plot idiot ball. You were fighting against Cerberus, and the Geth, not the Reapers. But the real enemy was the Reapers, but we didn't know that. We thought we were winning. Humans, Turians, and now the Asari were getting harvested. The Batarians had been conquered and were being harvested. But Shepard was winning every single encounter. Your multi-player map showed that we were winning if you played multi-player. And now suddenly we find out that we're going to lose the war because the scene had us snatch defeat from the jaws of victory by being stupid. Bad writing is bad writing.
One could have written a line from one of your sidekicks "don't you think we should look at this on board the ship?" And have Shepard be a bit arrogant about it and pay the price. But I seriously doubt that there would be anything more than "download this, and let's get the hell out of here." EDI could crack the security protocol.
There should have been some mission failures before this. A couple more missions like Jacob's except where you were evacuating key people and weren't able to get to them before the reapers, or having to extract before your positions were overrun.