I see no problem in the tone & feel of the films. Problem is the horrible script and that they resort to rehashing old stuff, down to rehashing entire scenes.
ST09 greatest problem was the fuckload of contrivances that moved the plot forward, and the lack of character development. Ironically, STD acknowledges the latter because the characters realize nuKirk is still a dumb hotshot. But at least the film was somehow original, despite giving in to the prequel/reboot craze.
STD has a nice scope and all, but it was absolutely unneccessarry that the villain needed to be Khan. And it was absolutely unneccessarryy to put the climax from TWOK as the climax of STD. Whoo, they reversed the roles. Big fucking deal, it was still an uninspired ripoff. And you realize that the convoluted story was way too complex even for the writers to understand.
I blame Lindelof. He was the one who fucked up Prometheus with the unnnecccesssarrry Alien plot and the utterly stupid characters who basically killed themselves because they went full retard. And apparently he was also the one fighting for Khan in this film.