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What is "Classic"?
The term "Classic EverQuest" has two meanings. First, it describes the period of EverQuest when Brad McQuaid was in charge, the period from the game's launch until the release of the Shadows of Luclin expansion. It is also sometimes used to refer to just the period from launch until the release of the Ruins of Kunark expansion, but that is more commonly referred to as "Vanilla" EverQuest.
The people behind Project 1999 feel that this was the "Golden Era" of EverQuest, and have devoted a great deal of time and effort to re-create that period for others to enjoy. 
Why Isn't Everything Classic?
The entire goal of Project 1999 is to re-create classic EverQuest as faithfully as possible. However, there are many differences between Project 1999 and what was actually seen during that era on Live, for a variety of reasons.
For a list of the "nonclassic" bits, see the Non-Classic Compendium.