Beyond the bare minimum needed to run a game (skills lists, combat rules, etc.), my version would be structured thus:
1) I wouldn't include material that has been gathered elswhere, such as the Spell Compendium, or for which a Compendium is being planned (such as for Feats or Classes, if such are in the works).
2) I'd compile the Feats as a comprehensive chart with page references with symbols denoting campaign settings (if any).
3) I'd compile the Classes, broken down alphabetically as a list with page references with symbols denoting base archetype (Warriors, Priests, Arcane Casters, etc.).
4) It would include master weapons, armor and equipment lists.
5) A revised glossary.
6) Special attention would be paid to clarifying contentious rules issues- essentially becoming the replacement for the FAQ and other (occasionally) conflicting rules corrections, interpretations, and eratta.