For me, the 'science' part of Star Trek has always been about the rationalization of esthetic decisions. That's why I like it better than more 'pure' science fiction. ST does what they think looks cool and tries to explain it as realistically as possible rather than trying to make their very best guess as to what the future would really be like. The trick is making those explanations plausible. If we come away from the movie thinking that the Vengeance looked the way it did because JJ said "Just give me something bigger, much bigger, than the Enterprise. And dark. And scary!" instead of giving some more authority to his designers and technical advisers on how it would most likely look, then I'll be disappointed.
Say what you will about TNG but at least early on, there was a sense that they were thinking hard about these things and trying to be consistent and realistic. At their worst, some of the shows and movies clearly didn't care about established continuity, or even basic physics. That tends to diminish the enjoyment.