This is what I did, and why I did it.
Most of the fluff goes towards the back of the book. This is a direct result of extensive playtesting. The majority of players questioned preferred to learn a system by first generating a character. They also disliked having to wade through the 300 pages of fluff (a la White Wolf) to get to that section. This gave me a general order to the main Codex: character creation, other mechanics, then setting.
Character creation is done in the order that involves the least amount of flipping back to earlier sections of the book. Many parts of Midian's character generation can affect other parts. For example, picking the Formourian Soldier class gives a +2 to Stamina. Guidelines for interaction, combat, and the like follow character creation: it is assumed that one puts the horse before the cart. That also gives a gentler easing into the crunchy bits. Choosing a species for a character is largely descriptive, but combat rules are pure crunch.
Most of the setting information is embedded throughout the text. This is deliberate. Midian is designed so that system and setting are one. This is more than the implied setting common to fantasy games, and more than awareness of the logical results of the system's physical effects on the setting. The whole is integrated from the ground up, from the earliest stages. The downside of this approach is it is very difficult--and rather unsatisfying--to try to migrate the system to an alternate setting, or to use a different system with the same world. That is, Midian doesn't work well in Middle Earth, nor does d20 work well in the world of Midian. Setting elements that were not easily embedded in the rest of the text--or simply worked best separately (such as the history section)--were given their own chapters at the end of the book.
There is no sample adventure. This is intentional. Midian is designed to be more of a sandbox type setting, and less of a thematic one. That is, I created it to have a place to run around in for whatever adventures I wanted, rather than a place to follow a solitary metaplot. A sample adventure would push new players into a specific direction--intentionally or not--and I didn't want to do that. I also assumed that Midian would not be someone's first roleplaying game, and they would already have some idea of what an adventure was, how their troupe preferred handling things, and how to read a D4. I have since been proven quite wrong in that, but Midian is still lousy for handling the dungeon crawl (or re-skinned dungeon crawl) type of sample adventure. There will someday be a sample adventure designed for first-time GM's and players, but that project is already far more involved than what would be appropriate as an introduction in the main book.
There really isn't any game fiction, unless one counts the history chapter (but that's mostly a monologue) or the intro to the combat chapter (but that's at the level of the game table). Both of these are meant more as silly (or gallows) humour. Neither are introductions to the book proper.
The very back of the book is the glossary of terms. It's easier to find there, and terms are described as encountered.