Franchise movies are very much like romantic comedies, in that the structure is pretty much fixed and the fun part is getting to the end all in one piece - Boy has to meet the girl upfront and he has to end up with her in the end. This canon cannot be changed and the 'how' becomes the movie. Similarly with the franchise movies - Superman, Batman, Ironman, and other extra-mortal and non-mortal men. Nobody is going anywhere, nobody is letting any harm done to them, they remain in the same state as they started off at and they continue on with their adventures till they remain profitable. Even then, they are never completely taken off the roster; they are benched temporarily till such time as another new age director discovers a fresh way of bringing them back with some contemporaneous currency, and the saga continues again. Effectively, the business controls the creative here, preventing the fertile imaginations from running away with their crazy and daring ideas...unless someone is bold enough (and that someone is definitely a studio head) to deal the end game to character and be done with it. Conan Doyle had the guts to kill of Sherlock Holmes, Superman is killed off in a story arc, Nolan almost almost tasted the Holy Grail in 'The Dark Knight'. But it is reasonable to say that in this current climate of great financial uncertainty, studios would never risk running a character into the ground in the spirit of staying true to the story. There was a brief time in the history of Hollywood, during the 70s, when such bold moves would have been possible, where no character was safe and box office never came in the way of aspiring for greatness. But no Sir, not now! One can rest assured that the same characters that entertained one generation would continue to regale many more generations to come. It is like that line in the song 'Hotel California' - 'you can check out anytime you like, but you can never leave!'.
But that is not always a bad thing as the current adventure of the Enterprise proves. All the preamble above is warranted in order to have a greater appreciation of the creative constraints that the writers are burdened with when dealing with these serial entertainers. While the origin stories are relatively easy and fun (which is the only point where certain amount of license and freedom can be had, and that is the reason why the new directors helming the reboot of the franchise choose to start at ground zero, and not continue from where the previous one left off), the follow up to the origin story is probably the toughest task in town, as there is no longer the freshness and anticipation in the discovery of the characters for the first time, and the characters have to hand off to the subsequent installments with zero body count, and all the conflicts, tensions and frictions have to be resolved within the same movie so that there is no carryover to the next installment (in case, God forbid, there is no next installment owing to a poor box office showing) and all this, while having enough fun. This is what makes it 'Into the Darkness' a worthwhile time both for the makers and the audiences, as the makers seemed to have 'cracked the code' in delivering a movie, despite all its shackles, that is adventurous, fun filled and suspenseful (even when knowing all the while that nobody is getting bumped off).
The 'alternate timeline' idea that Abrams and his crew hit upon in the first installment (well, to be honest, they already tapped this vein in their TV series 'Lost') is going to be the key that opens up a wide variety of options and possibilities in taking the franchise forward. With this strategy, the current issue can remain true to the original and yet explore the old themes and ideas in a new light, where heroes can become villains and vice versa. It is almost a given that the two Spocks are going to lock horns in some subsequent edition (Leonard Nimoy's health holding up, that is) or Kirk is going to go rogue only to be brought back by his doppleganger in the alternate timeline (or even his successors from the future) or Klingon is going to befriend the Enterprise for warding off a super villain threatening to blow it all up till Big Bang come. Decades worth of old story lines and ideas are there for the taking, only to see themselves recast in this new 'alternate' limelight. All that the makers have to ensure is the directives be strictly adhered to - nobody is going anywhere, nobody is going to get seriously hurt and all would be well with the world at the end of the movie. In some situations as these, directives and constraints and shackles are the writers' best friends, a blessing of sorts that'll keep them from straying away from the preordained path. The current issue of Star Trek is a retelling alright, boldly going where it already had been before, exploring themes that it already did, but as 'Into the Darkness' proves, there is fun that could be had in these re-voyages.
Note to Hollywood: Three things need to happen in great haste that would gurantee even more billions and trillions that the industry is already miniting all around the globe - Michael Bay be given not a penny more than 20 million dollars for all his future ventures, Paul Greengrass be urgently introduced to the wonders and benefits of a Steadicam, and JJ Abrams be supplied lens-flare resistant film stock only.