While I can't speak on Frictionals behalf, I'll just throw my 2 cents in here.
Regarding your first two points, I would guess it's probably due partly to time and engine limits, and partly to realism. It is really hard to pull feet off realistically, and our built-in recognition of how a human being "should look" will quickly figure out that "hmm, those legs don't look quite right...". That is actually a quite large pitfall of loads of those "realistic" modern FPS games. As for the shadows, that would take a large amount of effort on Frictionals part proportional to the gain achieved.
Now, the last point, I frankly don't understand. Not as in "I don't understand what you're saying", but more like "Why would you even want that??". What you're suggesting here, and what I've seen you suggesting loads of other places around here, is to basically drag all these horror clichès into Amnesia... That doesn't make sense at all! Amnesia is all about creating an unique horror experience, and clichès are
not scary... Ravens, bats, little girls, mummies, they've all been done a million times over. They've become something we're all familiar with, and familiarity isn't scary.
Also, from a pure technical aspect, imagine how much work it would be just to create these. They'd have to create a model, texture it, animate it, make a new AI for flying creatures, test it all in-game to make sure it works, and all this for something that have been seen so many times before that it's lost any horror aspect it may have once had.
No offense man, but these ideas are pretty stupid...