On the face of it,
Star Trek Into Darkness had the potential to do what Star Trek has always done as far back as the 1960s, what Gene Roddenberry always said it did: shine a light on the social issues of our time under the guise of a science fiction allegory. The fundamental story behind
STID, the core of the plot as it were, is a post War On Terror story of who can we trust, and how do we adapt to a world after a cataclysmic change. The idea of a 'rogue element' within Starfleet working overtly to undermine the organisation, nay even society itself, and (most tellingly) the assassination/terrorist attack on the Admiralty, are all powerful ideas for such a story. On this level, 'John Harrison' is a fundamentalist terrorist, and the great moral dilemma for Captain Kirk is whether to trust Harrison, or to follow Marcus' orders. In some ways the story writes itself. It's a very traditional, very Star Trek-y idea. I can't help feeling that shoe-horning Khan into that plot did not do the story much of a service, and may in fact have detracted from letting it reach a fuller potential than it actually did.

Because the moment you make the villain Khan, then all the baggage that is associated with that character is brought to the fore, good and bad; and instead of it being an allegory of current events ('sleeper cells full of lone wolf agents take down a society from within -- how does Kirk
respond to that moral dilemma?'), we are instead invited to just say, ''Hey, cool, it's Khan!'', and laugh along at all the
TWOK allusions.
I haven't yet met anybody who doesn't think removing Khan from the equation could have resulted in a stronger movie. And I say that as somebody who
liked Star Trek Into Darkness and who thought Cumberbatch was great as the villain. I just feel that the villain who he was playing shouldn't have been Khan.
