1. No worries about the copyright, I'd say; you can get Cyan's permission to use their stuff by getting a Fan Created Content license. (You'll need one of those anyway if you're planning to share your Age publicly.)
2. NOT THE CRYSTAAALLLSSS! Repeat after me, "Crystals do not give magical powers. They are rocks. Crystals do not give magical powers. They are rocks. Crystals do not give magical powers. They are rocks."
3. About the people running around--that is probably next to impossible to do with our current technology. You see, it's very very difficult to create animations, including people moving around, doorknobs turning, mist swirling, tides coming and going, gears rotating, a sun crossing the sky, etc. All you can really do in terms of animation is to create kickables, such as beach balls, or have the avatar perform a standard animation such as swimming, running, jumping, etc.
4. For a reason as to why there are no people, maybe a disease (I'm thinking of the Irish potatoe famine) attacked their staple food source so they had to leave to find new food to eat?