Okay, I've done some research on the current quicktime encoding. It's still just a package of random types of media strung together, which is why Apple TV won't play them. One .mov file can have lots of different types of encodings in it and even different dimensioned files.

MOV is old, but it's constantly evolving. Apple is the one always pushing new and better technology and H.264 is the default encoding for MOV files in QT Pro. H.264 is actually newer than MP4 (not sure where your info came from) and is a better compression scheme. MP4 is an export option, but not the default. Most H.264 encoded movies (from DVD rips) have a MP4 extension and when I saw the H.264 encoding in quicktime I thought that it would do the same, it's not. It's an mp4 inside of a mov package.