Sony does have a better brand image, just like Nintendo. I know many people who were "waiting for PS3" even before they knew what the specs were. They, like Nintendo fans, had pre-decided to buy. Sure, MS has this too, but it's a comparatively smaller percentage, especially given how much the PS/2 outsold them.
Sony has franchise exclusive content like Nintendo, that has a large following. FF, MGS, GT. MS has Halo primarily, and Halo doesn't have the reach that brands like FF, MGS, Mario, Zelda, etc have. This has a big influence on many buyers, who would otherwise go for the cheapest console. It is especially a big loss for MS in Japan.
Microsoft doesn't exactly have a slick "consumer" brand image, like Sony, Samsung, et al. Most consumer's image of MS is colored by Windows.
Sony has an uphill battle on economic factors because MS has the better production economics. But Microsoft's brand image, even in the US, isn't exactly "living room" no matter how much they try to sell you the idea that MCE PCs are invading living rooms. MS has a long way to go to convince people that they are 'cool/hip' electronics, like Apple, Nintendo, Sony, and other asian and european manufacturers.
If I had to make an analog, I'd say that MS is like Ford trying to convince buyers that their latest sports car has the same style appeal as brands from BMW or Nissan. Ford actually has made amazing strides in the last 2 decades in terms of quality and design, but people still view American car brands as pedestrian, boring.