I don't think they made the movie TWOK. They made one scene a copy of TWOK, and it was a misfire that pulled me out of the story; but the rest of it felt fresh and very different from TWOK. I mean, Kirk and Khan actually had multiple scenes face to face! Khan was actually sane, calculating and manipulative rather than a melodramatic nutcase! And he wasn't even the main villain this time -- Marcus was. In almost every respect, this was an entirely different, and IMHO better, story than TWOK; but unfortunately it did have one sequence that gratuitously copied TWOK, and that tends to overshadow the rest in many viewers' minds.
I feel like the main problem with both Trek 09 and STID is that they had good storyline ideas, but then no one went back to tighten up the nuts and bolts to make a good final product. It's like they were more interested in peppering gratuitous name-drops of other Trek series (including the one super awful scene in STID) and left out vetting bits and pieces that little tweaks to the script or dialogue or scenes might've done.
I don't know how much of this is the director and how much of it is in the writing, but it feels like a little more editorial care would've done wonders to tighten up the movie. Getting rid of that gratuitous scene, making Marcus's emphasis as villain more concrete, changing timescales so that everything's not rushed into a single day, etc.
I felt the same way about ST09, in that the flaws seemed to me to come from a lack of care on details than anything pertaining to Trek or continuity. I mean if Nero was okay with floating around for 25 years (or was in Rura Penthe for that long or whatever) I don't think that the story would've been that much more damaged by giving Kirk a somewhat more credible rise to captaincy, maybe inserting a couple montages between say the Kobayashi Maru face-off and the Vulcan system thing, or finishing off Nero and becoming captain.