What's with the second half collapses?

I get that McVay has made us one dimensional in a few of these games and eventually they pin their ears back and makes it almost impossible for stafford.

And I get that a well oiled offense is just setting up stuff for later so even if you think you are in it, they have another level.

But I still have to question, if we can hang with the niners, eagles, and colts for the first 2 quarters, why can't we for 4 quarters?