If you really wanted you could apply criteria like settlement in cities vs tribal encampments, whether they had stone buildings, whether they had written language etc (for ancient civs at least). For civs that currently exist in the real world, since we do not know the future, we must combine those criteria with things like length of existence, power, size and influence in the modern age...even though in 500 years we may look back and say other civs (less well-known now) should be civilisations in the game.
In any case, the whole issue is subjective, and it's probably best to apply common sense. People are going to want the more well-known and historically influential civs in the game, and i am no exception to that. Thus the decisions on who to include will reflect the general wishes of the target market to an extent. There are a few grey areas when it comes to deciding who should be in or out - and yes it is a subjective decision. The more civs that are in the game, the harder it is to balance. However, i do think they ship too few civs and leaders in the original game in order to sell x-packs. I think the number of civs in Civilisation III, including all x-packs, is an appropriate number.