IntelliJ has historically looked pretty native on MacOS X. At least until Yosemite pointlessly reskinned Aqua to look more ugly. Now I find myself quite happy that IntelliJ is not a native Mac app because I preferred the old look anyway :)

You can make the apps look native, if you really care. But in an era when web apps are the shizzle why would you even care? No web app even tries to look native. They just do their own thing and nobody cares.