TWOK had its imperfections, mostly small (why is searching for a "lifeless planet" so hard? why does Reliant
not have star charts of the Ceti Alpha system that would have told them something had happened? why do they not remember it's where Khan was stranded? etc.) -- but was mostly excellent despite them, with good character arcs, memorable performances, convincingly-sold action that doesn't try to pummel the audience into numbness, and a truly moving death scene for Spock. A moment whose power was mostly leached by the studio's subsequent greed, true, but still in itself a genuinely moving moment even if you hadn't watched the old series. It is really the only Trek film of either the original or TNG franchises that has won, and deserves, real recognition outside of the Trek fanbase.
STiD is in the main a collection of flaws in which a few good elements can be found, wrapped up in state-of-the-art effects. The state-of-the-art effects are what won it recognition outside fandomverse, but really only (I suspect more strongly with each passing month) briefly and for the same reason Charlie's Angels reboots make money: the flash. Flash has a way of fading quickly, and its having faded, it is no surprise that more people are noticing the plot is nonsensical, the action pretty much interchangeable with any other franchise, the character arcs unearned and the setting's universe cartoonified to an extreme degree.
I actually found the attempts to tie in to TWOK less offensive than some people did -- and STiD's share of the backlash ironic given how much the better of the two Abrams films it is -- but still think STiD fans comparing what's happening now to a few grousers in an ancient fanzine are kidding themselves. TWOK will still be remembered and STiD largely forgotten in another twenty years from now for simple reasons of decent filmmaking versus bad/mediocre filmmaking; the real service Abrams rendered was to remind people of the older, better film.