Rankings are subject to so many factors, I don't think any "list" should be taken too seriously. Whether its from this convention, contrived from a very few voters and not from the community as a whole, or on a web forum like this one where its 1 person giving their personal list, its all complete garbage.
The way I see it, J.J. was just being paid to make some blockbusters for Hollywood. He himself has stated he's not a fan of Star Trek and has no interest in it or its history. He makes movies that make money and that's enough for the industry to keep him in it. What he did with these 2 new releases is bring in a bunch of new people who are aware of Star Trek and will probably look further into the series now that they've been introduced to it which is something I'm sure most here would agree the scene needed very badly after the drop-off from the 90s.
The movie itself had a huge amount of plot holes and inconsistencies "KHAAAAAN" should've been "MARCUUUUS" since Khan had nothing to do with the circumstances surrounding Kirk's pseudo-death, but quite literally all the Star Trek movies have had inconsistencies to some degree. You can argue that the ones in STID are larger than in some others like STTMP but at that point, you're just grasping at straws.
What we should really take away from all this is that there is now a huge renewed interest in Star Trek as a franchise. The question now is what will we do with it? Personally, I think a new round of TV saturation is necessary to keep the momentum going. The numbers clearly point to a large audience ready to support the series while the studios sit and bicker about franchising rights and cock-blocking the ideas set forth by the previous casts.
Instead of directing hate towards other fans or differences in "what movie was better", perhaps we should direct this hate towards the studios for stifling the momentum being created by the new films and essentially killing off the "New Trek influx" before it can begin to thrive.