I don't have enough direct familiarity with these to know where the major differences lie. It's quite possible that the differences aren't in the charters themselves but in the state laws of Delaware and Virginia.
Why were Fannie Mae JPS included if they are equity holders and not Common?
Good question. This makes me think there might be some difference between Delaware and Virginia in how common shareholders are treated. It might be specific to the implied covenant of good faith and fair dealing too, because if I remember correctly the class wasn't officially defined until Lamberth had dismissed all the other claims (breach of contract, breach of fiduciary duty, etc.).