I just made a brief comment on twitter towards Cam Banks:
Here's a quick example of what I mean. We just released the 20th Anniversary Edition of Shadowrun (link is to PDF version). One of the chapters that I spent a lot of time tinkering with was the Skills chapter. Here's the fundamental problem with the Skills chapter, from an organizational/layout point of view: All of the skills have a short description that are of a similar length, but some skills have no additional rules, while others have a few hundred words of additional rules, and others have even more, plus some reference tables. Then, there are the general rules for how skills work, some sidebars with example power levels and the Skill Groups, some guidelines on the various types of skills, and finally, rules for using attributes in place of skills.
Note 1: For those of you with copy of the Shadowrun 20th Anniversary rulebook handy, when I say "Basic" I mean the descriptions starting with "Combat Active Skills" near the bottom of p. 121 and ending at the bottom of the first column of p. 127. The "Using" rules start with the Using Specific Skills header on p. 130 and continue until the end of the second column on p. 138.
Note 2:The organizational work I describe here is not necessarily the job of the graphic designer; depending on how production on a book works, this organization is probably handled first by the managing editor [or in Catalyst parlance, the "Line Developer"] or editor, and given to the graphic designer to implement. In the case of this title, I had a lot of latitude to make my own decisions for organization, with developer approval. Some graphic designers will consider this work not their responsibility, and in many situations, it wouldn't be.
There's one obvious choice on how to organize this chapter: put all the general purpose "these rules apply to all skills" early in the chapter, along with any tables/sidebars that list all the skills and how they relate to each other, along with what categories they fit in. I'd like to think this is a no-brainer.
Other slightly less obvious but still easy choices are: sandwich the more specific rules for using the Special groups of skills [Knowledge and Language] in between the "Basic" section and the "Using" section, and put the rules for using Attributes as Skills right at the back of the chapter. They're the most odd duck thing in the chapter, but they belong there more than in the Game Concepts chapter, as they're somewhat special case rules.
So the big question is: do you lump all the skills ["Basic"] and all of their specific rules/tables ["Using"] together, or do you break it out into two distinct sections? Some of the questions I ask myself whenever I have an organization question like this are: How is the book going to be used? Is this chapter mostly going to be read? Used during character generation only? Used during play only? Both play and chargen? How many questions do I have to ask myself to answer another question?
In the case of the Skills chapter, the "basic" short descriptions of each skill are heavily used during character creation ... but once you have a few games under your belt, you know what the skill is used for and probably won't need to refer to them often. The "Using" rules that you may only use once a session or every couple of sessions, however, those will be harder to memorize, and aren't as likely to be consulted during character generation. However, there's no doubt that both "sets" of rules are 100% tied to each other, and people will be flipping between the basic and advanced occasionally, if they are separated.
Looking at all that, I made the decision that the "Basic" rules should be distinct from the advanced "Using" rules. Now within those two sets, I have more decisions to make, primarily: how to organize the list of skills. Shadowrun skills are divided into categories, such as Combat, Social, Technical, etc. In previous editions those categories may have been slightly different, but there have always been categories. Within the categories, skills are alphabetized, and skills that have an entry in the "Using" section have a page reference to that section. This should work fine -- when making a character, you are often looking for certain types of skills at a time, and when skills are in categories it's easier to see how they relate to other similar skills; if the entire skill list were one big alphabetical list, you might think you need Intimidation when the skill you're really looking for is Leadership. With categories, those skills are much more likely to be within a few entries of each other, so it's easier to get the "big picture" of what a category represents and how it's broken down.
Now for the "Using" section, which frankly, was a mess in the original ["green"] versions of Shadowrun, Fourth Edition. How to fix it? First off, I put "Using" in front of every single entry: "Using Etiquette," "Using Jumping," "Using Survival," etc. Yeah, there's some slightly odd phrasing in those, but by putting the "Using" in front of every header I was able to differentiate every single one of them from their "Basic" descriptions, to make cross-referencing easier.
One major decision for the "Using" section -- do I break these skills down by category, or just alphabetize them all? I chose to alphabetize them all, because this is a section that you aren't likely to read straight through, comparing and contrasting. This is a reference section. You use it when the boat that your 'runner was on just burst into flames and you jumped into the water and need to stay afloat: you're looking for Swimming first, not Physical Active Skills, and when actually using the skill, the category rarely matters.
Then came adding in what I refer to as "signposts," a subset of cross-references. Here's the easiest example of a signpost, and why it's in the book: there's a header named Using Build or Repair that does nothing but point you to the header Using Technical Skills to Build or Repair. Why do this? Because players looking to Build to Repair something are likely going to look there first, especially if they are players of Shadowrun First through Third Edition, when every skill had a "Build/Repair" specialization, discussed in a distinct section. Yup, some people might consider those two lines in the book "wasted," but I consider it space well spent.
Some of these signposts also point to subsections like Using Charisma-linked Skills, which covers such skills as Con, Intimidation, etc - so if you flip to Using Intimidation, you get pointed to the correct page, not left in the middle of a field with a broken GPS and no cel-phone signal. And some of them go right to other chapters -- such as the rules for spellcasting, which are intricate enough to be in the Magic / Awakened World chapter.
I hope this sheds some insight on how and why some organizational/layout decisions are made for a gaming book. It's a matter of give and take -- balancing organization, fitting all the text in, fitting in artwork, keeping things looking "cool," while maintaining the utility of text/tables/diagrams. There's no "one true way" for organizing a game book, or any other book -- but the right way to figure out the best way for any particular title is to identify how the book [or a particular section of it] will be used, and go from there!