I'm in the middle of re-doing our intraweb page from the buttons on the left configuration to one that looks like your standard Yahoo portal. The reasoning behind the change is to reduce the number of mouse clicks required to get to the information the customer wants/needs. The goal is to find what they need in one or two clicks.
Of course, creating a page that literally has links to every document on the site soon becomes very messy and difficult to find what you want. So the Yahoo model of efficiency has to be balanced against the practical matter of having too much information to sift through.
Part one of the project was to create a page with all the links on it. Part two will be to organize the links in ways that people will find easy to get to where they want. As tedious and slow going as part one was, part two will be even more challenging because people deal with information in different ways.
Some people are visceral. They go through life as a mass of emotions, feelings, and impressions. They solve problems in a round about way that seemingly has no rational process to it and is characterized by leaps from start to conclusion.
On the other hand, some people are rational and logical. They analyze life by breaking down the whole into manageable problems, studying these problems, generating hypotheses, establishing objective criteria, deciding on a solution, and then evaluating the results of the solution. To these people, problem solving is a straight line process.
To create a web page that satisfies both is difficult, if not impossible. But as far as I see it, a web site with a logical system of folders and sub-folders would drive the visceral person to distraction. Conversely, a portal site where everything is everywhere will frustrate the logical person.
In the end, the best way may be a dual site and let the user pick which path to follow.
Aloha!