Ok first off, I don't believe that coding a little flashing save icon can possibly cost so much time and money for it to be of any significance in the budget of an AAA title.
Secondly, while I have always felt that each and everyone should be allowed to express their views on gaming, I feel that Jonathan Blow is getting a little bit too much attention. I mean, he only made, as far as I am aware, one single game, not matter how good it was. In fact, I find it especially excruciating to have to listen to this guy's opinion of how the industry should deal with saves, considering his "magnum opus" only allowed for one, single save at one time. I mean, come on ! If your game is so blasted clever, why do you have to make it such pain for me to show it off to my friends and family (because if Braid is such an "experience", you'll want people to try it from the start, right ?)
I just looked into the game files : ok, granted, there is no separate file for the saves, so it's not just a matter of "why the hell couldn't I choose from different files/folders (I'm looking at you, Bastion, but I still love you). Still, if you can code saves, you can code a way to have several of them.
Now, as to his actual idea on saves : is this guy really going to say the main problem with the corruption of save files is the "save" icon ? Isn't the main problem the fact that many games always overwrite the same file over and over again ? Which makes it possible to put the game in an unwinnable state without any sort of bug (fucking Overlord II) ?
I find this guy just criticized the one part of most console's saving system that isn't broken.
When it comes to how to fix it, I say, look at Skyrim : have a rotation of, say, 3 autosaves. If one gets corrupted, you loose from 10 seconds to 10 minutes of gameplay, no harm done.