I've always believed strongly that a native UI presents a cleaner, more consistent, and more beautiful interface for the user to interact with. Not only do they look better, but they present less of a learning curve because the user already knows how to interact with them. When applications move beyond competing to see who can make a better home-made button, they can focus on greater underlying functionality and stop wasting time reinventing the wheel that the operating system already provides.
Leadwerks 3 uses the native UI on both Windows and OSX, and it's turning out really beautiful. Since one picture = 1000 words, I'm going to let the images do the rest of the talking.