In mega-sites, the website's chaotic nature often reflects the size and complexity of the business itself. Upgrading the website in a significant way can require corporate change - and that's a tough nut to crack. Internal company politics can get in the way - as well as nearly antique "models" of how business should be run. A good example of a company that runs differently and therefore succeeded on the web is Zappos.
It's a funny thing, but even a one person "web team" can show the same patterns. It's as if that person has several internal fragments and they don't communicate well with each other. One fragment might be very visitor oriented and the other is search engine focused. But unless the person pushes each fragment toward a robust understanding of its focus area, they will undermine each other.
A classic example of this is following a particular list of "SEO actions" in a rote fashion - adopting the latest SEO buzz in a blind fashion. Many smaller sites actually hurt themselves trying to do "PR sculpting" or using the canonical link tag. It would have been better for those webmasters if they never heard of the concepts.
When it comes to the microsoft.com site, I am a little surprised that they still use the URL to track the user's click path. They know about it, and they don't use the canonical link element (or haven't been able to). They have canonical issues all over the place, beginning with "/" and "/default.aspx"
Wheeler really has his hands full just trying to prioritize that pile of problems!