There will be no bad guys in a normal sence of the two words. There will be different world view. As Israel, palestinians may be refered to as terrorists. For Iran, who gives support to Hamas, they will be freedom fighters. As the UK (due to tensions) Russia may be precived as the bad guy. As Russia, it will be the EU / USA (NATO) which are expanding into their backwaters despite early 90's agreements.
In a world with many viewpoints, we as modders can't choose the one we see most fitting and present it to the people playing. It would still be subjective. I as an supporter of Iran's nuclear program, should not be painting their arguments all over in the mod. However, we will show the different sides to different countries.
You can look forward to 1.60. It will have a real storyline, more realistic units and combat, more countries, more things happening, a whole new interface and graphics, leaders, tech-teams, techs, ministers, elections and AI.