Does that mean the film will focus on Khan? Probably not... Orci stated, "We would never do a remake… it will be some time in the five-year mission. But that is a question. Should we pick them up immediately the next day or should it be later? We are still discussing that." However, he did say that the villain will be the most important part of the sequel.
Spock actor, Zachary Quinto, also remained elusive in his response to questions on Spock versus Khan by stating, "I don't know man, I don't know. I'm just excited. My focus is elsewhere and I know that when the time is right and they want me to be involved again ... Until then, I love to let them do their thing because I know that what they're doing is really exciting but also really fun. They're good people."
Whether the film will feature Khan or not, I'm sure that Abrams will be able to pull off a wonderful epic again. Definitely one of the few sequels I am excited about, Star Trek will roll out to theaters on June 29th, 2010 (expectedly).