j.j. and crew went so far out of their way to establish a new universe and opportunities for the reboot that it just seems like a total cop-out to rehash the khan character. even if it is a different story.
Can you think of any better villian in the entire history of the franchise than Khan? Even the Borg - which at one point were great villians - were completely defanged by the end of Voyager.
now using section 31 and a rogue admiral marcus is a cool plot move.
One of the great parts of section 31 IMO is it portaryed a more realistic version of any large military organization where some people have an alternative and often darker agenda. The real life parallel in the US of course is Gitmo and torture.
Star Fleet up until they introduced section 31 in DS9 was essentially a bunch of unrealistic goodie two shoe characters prancing around the galaxy proclaming how superior their values were - which of course isn't a realistic version of how people are in real life.