Haven't got far into the game so can't answer your first question, but regarding Cleopatra: she was to be joint ruler with one of her younger brothers because it was in her father's (the previous pharaoh) will. Female pharaohs were uncommon but they did happen. Normally a male heir would be named as the next pharoah, and if he was too young to rule but had an elder sister she would be named regent and assist with ruling until her brother was old enough to rule by himself. So Cleopatra was already lucky to be named as joint ruler, but that wasn't enough for her. She plotted to murder her younger brothers so she could rule solo. Hence being outcast when the plans didn't work... flawlessly.
Also, Hatshepsut was a female pharaoh and is widely considered one of the best pharaohs Egypt ever had. Highly focused on trade and infrastructure. Nefertiti is another famous female pharoah, ruling jointly with her brother/husband Akhenaten, they were... less popular. They decided they'd move the capital of Egypt way out into the desert, abandon all existing gods and outlaw their worship, and create a new single god instead - the Aten, the sun god. They also decided to cut ties with all their foreign allies, focus entirely on Egypt and what's best for Egyptians, and like all the other times in history that isolationism happened, it ended pretty badly for everyone. That was over 3000 years ago. Some things never change =P
