In the real world, vanilla is the most common flavor of ice cream, not because it is strongly loved, but because it has a mild taste that few people dislike. It is considered the "default" ice cream flavor. By analogy, the term "vanilla" is used in many domains with multiple versions of a thing, as a synonym for "plain" or "default".
Among EU2 players, saying "vanilla" or "vanilla EU2" is way of making clear that you are talking about unmodified EU2. Furthermore, for the purposes of this wiki, vanilla EU2 also means EU2 1.09. Any pages which discuss the various mods (such as AGCEEP), or EU2 with patches older than 1.09, should carefully mark such information.