I've been thinking about it and if there's one thing I can get behind with the soulless action movies currently lurching around in the flayed skin of Star Trek its that the writers seemed to have largely dumped the Prime Directive.
Now, as a general case the PD is very high-minded and enlightened in a 1960s end-of-empires sort of way. Its there to show that humanity has learnt its lessons about just blithely destroying indigenous cultures and that just interacting with a new culture comes with moral responsibility.
However, looking back at it the PD was usually used as a cop-out so writers could avoid the consequences of confronting actual moral obscenities. If that seems like a harsh judgement on my part then look at any Voyager episode featuring the Vidiians. Yes, they're murderous organ-harvesters but but only because of the chronic flesh-eating disease they suffer from and yet Captain Janeway continuously refuses to offer them medical or humanitarian aid. The disease, by the way, turns out to be curable (there's a throwaway line about it in Think Tank). Its even worse in the early seasons of The Next Generation which all too often devolved into Picard and his crew very high-mindedly doing nothing and congratulate themselves on how moral they are as material suffering continues off-screen.
Now, the Prime Directive does feature in Into Darkness but only in its First Contact form (the episode, not the movie): you don't let pre-warp cultures know there's more out there because they have to make those discoveries on their own. The version where you just fly past atrocities, however, seems to have been left behind and I can't say I'm disappointed.
Now all we need is a movie that actually has something to say about... anything, really. Neither Star Trek (2009) or Into Darkness had much political or philosophical content to play with.