Look, I hate IE6 as much as the next developer, but it's important to recognize the difference between the thought process that goes into making comercial products and making new tech ideas. MS figured out how to make the most money they could off technology. They are (were?) damn good at that.
But despite all the seemingly stupid tech decisions they've made on many consumer products they still have some brilliant people working for them, esspecially in R and D. I have a hard time thinking that the PhDs doing research for Microsoft are unaware of the mistakes/limitations of IE (in all its forms). Yes, the funding for this research comes from Windows and Office, but it has more of a chance of seeing the light of day than something done in a strictly academic environment.
For better or worse, MS is going to try to do whatever is going to be best for MS. Hopefully the big brains that they have at their disposal will be able to make a good commercial case for better ideas so that the general public can reap their benefits.