Both are messy but First Contact is the superior film, and one of the better Star Trek movies. I really like the interactions between Picard and Lily, and how the movie didn't just try to ape the previous Borg stories. Star Trek Into Darkness was just a copy-and-paste job of the previous movie and Wrath of Khan.
This is about how I feel, which is also how I feel about Nemesis. Even though they're two "different series", giving a copy paste movie of WoK in 2 out of the last 3 trek movies...and in a lot of ways Star Trek 2009 was the same plot in essence (superior being trying to get revenge), it'd be nice if they took some other base plot.
Back to the special features, they talked a lot about the Picard/Lily relationship and how she presented such a foil for his Ahab-style hunt. First draft apparently have her as a love interest, which I'm glad they took out. That would have been too much. The character of Lily both from a writing and acting perspective was pretty great.