TJ Spyke's post here.
McDonalds claims that the menu was in the works during the film's development. It's conceivable, but by no means provable that the menu was going to change regardless of Spurlock's movie. McDonalds did deny it. It's their word versus yours, essentially. I'm not going to try to determine how long it takes a food item to be conceived, then placed on menus nationwide at a large chain. I will note, though, that my town was a test-market for Hardee's Thickburger sandwiches back before they were all over the place. Those things were probably around at least half a year, if not more, before they were placed on the menu permanently. Don't believe restaurant menus for places like McDonalds are taken lightly and modified on whims.
Additionally, the other items you quote weren't on the menu at the time Super Size Me was filmed. The milkshake was, the rest weren't, at least not nationwide.
As far as fries go, I would imagine this would be the result for a number of salty foods. While I've done absolutely no research, I do know that osmosis takes place, and salt on the outside of the fry would result in the fry drying out much more rapidly than anything else placed in containers, which potentially means most moisture could've left before the fries were enclosed. Of course, Spurlock and his crew didn't do any actual research or testing either, so I suppose I might be as much of an authority on the matter of what happens to fries over a few weeks as he is.
I honestly don't recall that part of the movie, though. I'm really surprised to hear that something enclosed in a container could be smelt. I would think the purpose of the container would be to keep the contents closed, air-tight, to show what happens to them over time. If the food smelled bad, then that means the containers weren't air-tight. If the containers weren't air-tight, given what a few recent things have shown, the food (at least the smaller burgers, and definitely the fries), should not have grown mold or anything, and instead should have stayed well preserved. That's what those foods would typically do, at least according to light research I've read over the hubbub of that woman and her McDonalds "experiment." Did Spurlock or the movie say the conditions under which the food was kept? If he suggested they were sealed, but were later thrown out because of scent, then they weren't sealed. I'm a little confused as to what you're suggesting he's suggesting, regardless.