The codex style should really only be used to fill in extra info that doesn't affect major story lines. It should give historical details, odd facts, enemy info and updated info on characters as you learn it. Basically, things that enrich the world and lore.

If you need to go to the codex to understand major plot holes, there's a problem. That was one of my problems with FFXII and XIII, aside from what I thought were subpar stories, ability systems and battle systems.