With security and data transfer concerns are less of a headache, you can have a more 'feature-filled' intranet webpages that can do 'safe' thing like automated unsigned ActiveX executions etc. combined with HTML 3.xx standard pages. I know that isn't safe at all, but these kind of crufty websites are way too prevalent in company networks across the world, and more often than not, works fine in IE6-only browser. This kind of browser-based applications will not just be upgraded like that especially in conservative IT environment, just like what motherboard makers tell you about BIOS upgrades (do not upgrade if nothing is broken). HTML/CSS of those old applications can't just be treated the same way Internet HTML/CSS do, because it will certainly break. Now, if those Intranet webpages are standard-compliant in the first place, there there is no problem switching on standard-compliant mode in Intranet zone, but it seems that Microsoft think that there are many intranet pages out there that are not upgraded yet (and I do share the same opinion), thus compatibility mode is set to default.
For Internet websites, there are incentives for webmasters to follow W3C recommendations, as it allows them to reach more people with different browsers. Intranet websites, there are no such incentives in a highly-controlled environment, where IT/HR departments can simply tell the workers to use IE.
Plus, more importantly, Intranet zone can use standard mode anyway. Microsoft probably could have defaulted Intranet pages to use standard mode (after all, changing to compatibility mode for Intranet zone seems to be as easy as flipping a switch in Group Policy). You have to consider that unlike home users (who mostly have no use for Intranet zone - thus Microsoft can force), browsers in enterprise networks are tightly controlled and settings can be pretty brutal. So, in the unlikeliest chance that the companies actually upgrade those Intranet webpages to be standard-compliant, the drones at IT department can easily turn on standard mode later.