1. They should not do Khan again. Or any other TOS story line. this is a chance to take ST in new directions and it shouldn't be squandered re-making the stories we've already seen.
2. The history of the ST universe isn't the history we live in. We live in a world where the events of ST have taken place on TV and movie screens. ST takes place in a world where that stuff actually happened in real life in the 22nd, 23rd, and 24th centuries. In their history the Eugenics Wars DID happen, but that does not need to mean it did in ours. And apparaently it didn't.