The iTunes files are PLUS tracks which have no DRM and are encoded at 256kbit AAC.
Plus is nice. But converting to MP3 is still an extra step, which is (a) a pain, (b) another lossy generation, and (c) buying the Plus track still adds monetary and marketshare support to a system which continues to be rooted firmly in record-company-mandated DRM. These issues are unimportant to some, a marginal inconvenience to others, and a deal-breaker for a few.
The Amazon files also have no DRM and are 256kbit MP3.
Which I totally applaud Amazon for. Too bad they don't have the international side of things sewn up as nicely as Apple does.