The Kingdom of Heaven BD may lack the overture and intermission, but the picture quality makes up for it. The only reason the DVD had those interludes was because the DVD format itself made them split the film into two discs. Without that restriction, there is no need. Although I do enjoy the break. But I would never say that the DVD is better, simply because of the superior audio and video of the BD.
The Star Trek movies don't bother me, as the "directors cuts" were created for DVD anyway. Leave out the theatrical cut and the disc sucks, include the theatrical cut and the disc still sucks. It's true that they could have included both, but this is how the DVDs were anyway, with each cut it's own release--and the Blu-rays, despite some DVR, are way better than the 1990s DVDs which came out so early in the format. Like the DVDs, there will likely be expanded-cuts versions which have better picture due to later release.