We can try argue for reasons why certain parts of a costume should or shouldn't be kept, but when you get down to it, that's really a bit pointless, because we're trying to apply practicality to a deliberately unpractical outfit. Even though the Nolan films made a fun attempt at giving plausible reasons for different aspects of the costume, when you really look at these things in a realistic setting, it still falls apart. Take his cape. Sure, Batman's cape can allow him to glide, but it would still be a massive hindrance in a fight, and something that would probably just get him killed.
So when it comes down to it, it really just depends on what we think looks better. I don't really care about the costume with or without the trunks. The trunks in the comic were a necessity of design to brake up the shape of the body, and it made sense. In the films, we don't need that because it can be accomplished other ways. But I think the trunks could be done and still look okay in live action.