Ah, I apologize. I missed the part where you wrote 'Thousands of years went by'. xP My bad! 

What will the major factions be? I'm guessing they would be: 
- Human
- Bad guys Animals (What drove them to be the 'bad guys' though? Is it in the believe that they all would be better off without humans or because they wanted to rule over all?) 
- Neutral Animals (I'm guessing that they would be mostly defending themselves instead of outright aggressiveness?)
- Hermit/Lone soul Animals (I'm thinking these would be the ones with the principal: 'Leave me alone and I'll leave you alone.' )