There were also early rumors that the villain was Harry Mudd. Did anyone else catch the little shout-out to him? I giggled.

Dont talk about my outfits that way!

I feel like Into Darkness fell into the same trap that (as I understand it) Superman Returns did, where the movie is a squeal, the story is a remake and the characters are a reboot.

But Bryan Singer did apologize for essentially not keeping his ego in check with Superman, So maybe JJ will lighten up in a few years. Or not.

No no that sounds about right to me 

I'll put it in Matrix Reloaded territory, though its better than Iron Man 2 on the strength of its action sequences.

I think the disconnect is happening because most of the action sequences are impressive and well staged, and most of the throwaway character banter is fun and works. This, combined with the story approach of keeping the audience in the dark until 60% of the way into the movie, allows it to feel like the movie is working as you're watching it, because you're giving the movie the benefit of the doubt that it will all make sense and that the movie knows what its doing. I think this is why its so high on RT (I hope that number goes down after the weekend, lest the bar for what a "good" movie is drop even further).

Of course, what you realize when you walk out, is that basically everything related to the actual STORY of the movie is an absolute mess and fails miserably, and the stuff they pull in the 3rd act is such awful fan-wank bullshit that it kills any good will the movie may have built up. This REALLY feels like Crystal Skull in the way that there's multiple plotlines and character arcs that go completely no-where or just disappear from the movie.
I think the movie will only get worse on repeated viewings, and it seems dumber and dumber the more you think about it. So many stupid choices.