Actually, Cleopatra's lack of beauty has been known for some time. I recently read the book I, Claudius, and the author quotes ancient sources that Cleopatra was rather plain looking, but very winning through personality. Not to mention power as aphrodesiac: look at all the gorgeous models and even the actress Susan St. James who slept with Henry Kissinger. Yuck.
I Claudius was written in the 1920's, so for people who know their ancient history this is nothing new. But if Firaxis wants to portary her as beautiful, I'm fine with that. Its a minor thing, and sometimes falsehoods become so widely known that the truth seems like the lie. I'm sure Cleopatra will stay beautiful in future depictions, no matter what historians and archeologists dig up on the matter.
As for skin color, as long as they're reasonably close that's fine with me. Maybe she's just been out in the sun too much lately and gotten a strong tan!