Well, on paper something might seem better but really they're different tools for different needs.
The biggest one I can think of is the MkIV isn't full frame, it's an APS-H instead, this does have a knock on effect on specific types of photography (I'm not a great believer in all kinds of photography need full frame, but it certainly helps with landscapes and portrait/fashion work). The other knock on's come from that, lower noise at low ISO ranges, better image quality and better colour depth.
The MkIV however is ridiculously fast, shooting 10FPS, and can record 1080p HD video, and it's lighter, and it's got a much, much higher top ISO. And cheaper.
The 1DS pulls a higher premium as it's designed for a different kind of photographer, and the full frame image sensor probably adds a nice chunk on, where as the MkVI is designed as the go to camera for everyday pro's who don't necessarily need the bonus features of the 1DS MkIII in terms of image quality. It then becomes the economy of scale for Canon, they probably know they'll sell more, meaning they can take a lower price on it.