The cutscenes were stupid and the player knows the game will end three missions later, but put yourself in Shepards shoes. The mission was a failure. You've just lost to Kai Leng, failed to get the VI...and you have no clue where Kai Leng went. I think it's natural in that situation to ask yourself what you could have done differently.
Add to that that Thessia reminded Shepard of what happened to Earth (Shepards Earth centrism has been widely discussed in various threads) and how the war was already grinding on her mind (dreams) and you get a devastated Shepard. I think Bioware did good in stripping you of the choice of being a happy Shepard there. It wouldn't have made any sense.
Again, there's just too much dissonance when you're practically rubbing it in our faces how much Shepard utterly failed, even though it's all scripted, and thus you're basically saying the player failed.
"Thessia is lost, and that's on me!"
Since we are Shepard, that's like saying "Thessia is lost, and it's the player's fault!"
I don't care that in-character Shepard is feeling miserable for the loss of Thessia because I as the player don't feel miserable about it, I feel like I've been scolded and I'm angry. This is a game, first and foremost. There are certain conventions that need to be adhered to because of that. Fighting a boss only to do everything you can to win and getting a game over screen is bad game design, and that same logic applies in Mass Effect's narrative, because the narrative itself IS gameplay.
It's the same thing with the ventboy. I get that Shepard is flipping out over it, okay, but it's the fact that obviously I am supposed to be flipping out over it as the player, too. Like, I didn't know this kid, why should I care?
In both cases there is dissonance between what Shepard feels and what the player feels, and that's a result of bad writing.