This is where a Chapter Approved supplement for the codex would come in handy. The Codex Space Marines which would have basic unit descriptions (Captains, Chaplains, Librarians, Tactical Squads, etc), lists and stats, and fluff along with how to tips on assemble and paint your new army, then a supplement for each major "codex adherent" first founding chapter with their successor chapters, special characters and wargear, special units (like Tyrannic War Vets for the Ultramarines or Sanguinary Guard for Blood Angels, modifications to force organization charts (for those pesky Dark Angels Scouts that are not Troops, but Elites), suggested army lists, and appropriate fluff. So if you want to play Ultramarines or one of their many successors, you get the Codex plus Chapter Approved: Ultramarines. If you want to play Blood Angels or Fleshtearers, you get the Codex plus Chapter Approved: Blood Angels. Fancy a shadowy hit and run army? Then get the Raven Guard supplement. All this would be three-hole punched for placement in a binder. Seperate codexes for the two non-codex adherents (Space Wolves and Black Templars) would also work.

This could also work for the various Xenos armies, Guard, and Chaos. An Iyanden Eldar army would have access to some different units than a Biel Tan army for example. Supplements for Cadians, Catachans, Tallarns, Mordians, etc. could introduce new special characters and rules. Limitations could be added for certain factions that don't exist for others, even though both armies are the same race/group. The Inquisition could also be done the same way with seperate supplements for Grey Knights, Sisters, and Deathwatch as well as Custodes, Arbites, and Inquistor retinues.