I know I haven't really given much information on what is going on. I am sorry I had a lot of conflicting ideas and talked it over with a friend to get it straight. 

First off your character will be able to control elements based on their family. Like Dragon Roar usually control fire and so on. 
 The gems help you control the artifacts power without them it is hard to focus and maintain your control.

Most Digimon will hate humans because Legend hasn't favored them due to propaganda and only a select few of Digimon will know the truth of the warriors. The others will try and either kill you or capture you.