There are many ways to use modding. It can add things (new nations, new gods, new pretenders, new units, new disasters) or it can remove things (nations, pretenders, units, disasters). A mod can be used to create imbalances, or to create what a modder feels is better balance (mostly for testing and proving a point). A mod can be used by all players in a game in order to enforce house rules by removing something from play. A mod can be used in connection with a map to create a scenario game. Map commands can do alot toward creating opponents, but mod commands can go even farther.
And my favorite of all... a mod can be created on the fly by a very small and simple program to randomize one setting on every single unit in the game. Not for balance obviously altho since all units get the treatment there would be a balance in a manner of speaking. But for the new-game exploration of what you have to work with and what you might come up against. Its a favorite because it goes well with my site which is all about adding random surprises to the game.
www.dom2minions.com