Hello, and welcome to the forums!
It's totally possible to use pyrogenesis (our custom engine) and create a game with it. A lot of mechanics of the game, and also art, as Lion.Kanzen said, are outside of the engine and totally moddable.
You have the choice between creating a mod that will modify some things in the main game (all the current mods by the community do that) or replace the main game by yours. It all depends on how much your idea is different from 0 A.D. (is it historical, realistic, etc.) and on your interest in getting close to the development of 0 A.D. If you replace the main game by yours, you will not receive the updates and bugfixes we include in the main game, and I'm afraid you will not be able to go far especially if you are alone. It might be easier to create a mod on top of the main game.
Regarding the technology, all the mod programming is in Javascript. This forum has a lot of resources for everything art.
If you want to learn more, you can visit the wiki on our bugtracker, especially this page: http://trac.wildfiregames.com/wiki/GettingStartedProgrammers
You can also say hi on IRC, on the 0ad-dev channel on QuakeNet. Even if you don't want to contribute to 0 A.D., feedback from people who use the engine is always appreciated! And don't hesitate to ask if you have more specific questions.