Place tomatoes and tomatillos in a medium saucepan, cover with water. Bring it to a simmer and cook for about 10 minutes, or until tomatoes and tomatillos are soft, thoroughly cooked and mushy but not falling apart.
Remove tomatoes and tomatillos with a slotted spoon, and place them in the jar of a blender or food processor and process until smooth.
Heat the oil in a large and deep pan over medium heat; once it is hot but not smoking, stir in the onion and cook until soft and translucent, for about 5 to 6 minutes. Stir in the garlic and cook until the onion and garlic mixture becomes fragrant and lightly browned, about 1 minute.
Pour the tomato/tomatillo sauce on top and add the oregano, marjoram, thyme, salt, black pepper and the chipotle chiles in adobo sauce (if you want more heat add an entire chipotle chile in adobo sauce). Let it simmer, stirring now and then, until it seasons and deepens to a deep red color, about 10 to 12 minutes. You may want to partially cover the pan as the sauce will want to jump out onto your burners.
Add the shredded chicken and combine it with the sauce. Let it cook, occasionally stirring, until the chicken has absorbed almost all of the juices and the mixture is moist but not juicy.