I was initially confused as to the cause of the bad design, but I realized the corporate pressure was on the public site and there was less pressure to improve Intranets because they're hidden from public view. While a large number of Intranets are poorly designed there's an increasing number which are well-designed. The corporation mandates the use of templates to gain a consistent look, but can't force their users to adhere to more rigorous usability standards. Since access to Intranets is restricted from public view, I find it interesting so many Intranets share common design mistakes. There may also be political issues you just can't successfully fight.
Discretion is always the better part of valor.
That Suck and co-author of the book of the same name, lists the top 10 mistakes he's found while consulting for Fortune 1000 corporations. Corp. All Rights Reserved.