Although both sides appear totally different their is not much difference between them in conflict so when choosing sides it's basically just a matter of deciding whether you want to be the good guys or the bad guys. Regardless of your decision your focus should be on sending your troops out so they are able to complete the recommended quests in the building log so you earn the desired resources needed for research or upgrades so you are able to strengthen and build your base. Note: You will have absolutely no control over battles apart from being able to select how many troops you want to deploy.