I'm not quite sure about silent hill, but I'm sure there are reasons for Metal Gear Solid being missing. There's virtually no way to do an HD treatment on the original game, it's too dated and any attempt (short of completely remaking it) would look like crap. It MAY have been possible to HD-ify Twin Snakes, but there's a good chance Nintendo still has exclusive rights there. Obviously the Japanese got a download code for the original MGS, but I'd rather have Peace Walker anyhow.
Exactly. Both Silent Hill 1 and Metal Gear Solid 1 are PS1 games. There is just no way to HD them without a complete remake, and Nintendo does indeed own the exclusitivity for Twin Snakes. Konami was able to use a loophole in order to use the Twin Snakes audio in MGS4, but nothing else. They could have used a code, but then it'd almost be false marketing, because people would assume that everything in the case is HD.
In the case of the God of War Saga collection, I don't get the hate. Yes, the PSP games are downloads, yes, I try to avoid download only things as best as I can. However, the only other option is to add a second Blu-ray disc to the package, raising the cost. God of War III itself is over 32GB, as reported by Santa Monica, and God of War 1 and 2 both came on dual-layer DVDs, indicating that they are over 4.7GB as well. A look at sites of dubious legality gives a size of 18.57GB for the God of War Collection, 9.11 GB for Ghost of Sparta, and 7.37 GB for Chains of Olympus.
And honestly, if you have to have them on disc, like myself, there is a perfectly good collection disc already available...