I think the issue lies with the fact that the writers didn't let the characters speak. By that I mean, when I write I listen to my characters, I let them breathe. If the people that live in my head didn't want to do something, I didn't make them do it. As an example, Justin was originally going to curse Melissa in a fit of anger. It would have made for future angst and trouble and I would have had so much fun with it. However when writing Justin, I realized something. Justin would not curse another, not for any reason. He spoke very clearly to me about that, so I had to think of something else.
In Jupiter Ascending, Jupiter and Caine end up together, purely because the plot said so. Leaving aside the 'we spent two hours together and now it's love', there is very little chemistry between them and every bit of dialogue they utter on the subject seems forced and unnatural. I could have got behind sexual attraction (not that there was any signs of that) but not 'love'. Hell Jupiter even seems strangely okay with what's happened to her. I could have got behind building interest (see Replacement Killers for how you write growing attraction) Christ even Terminator managed to pull off a relationship that seemed natural. Possibly because Sarah Connor was confused and angered by the whole experience and she did step up and actually find her own salvation.
So what I'm really saying, if you genuinely want something to happen in your plot, don't force the characters into it. Actually step into their heads and work out how they would get there, don't make them walk where it makes no sense for them to walk.
And I know I'm a self published author but I would never do what the Warchowski's did. They could have had a brilliant sci-fi movie. They could have had a surefire hit on their hands, but they fluffed it. The writing is sub par, the 'romance' is risible and they waste plot threads.
What has Jupiter Ascending taught me? It's taught me to be logical and listen to my characters, not to get so carried away with my original idea, that my writing tanks out.