I don't like native GUIs, most OS GUIs look horrible, and I rather want some cool UI like in 3DSMax, Blender, Crysis or Delta Force.
No 3DSMax artist has complained that 3DSMax doesn't look so horrible like Windows XP, 7 or OSX, and I think for them the GUI look, feel and functionality is quite important since they use it for living.
And what would happen if the user (like hardcore users do), use a custom GUI in their OS, perhaps even a custom GUI engine, like most Windows skins do?
Would LE3 then be able to use that also, or would it fall back to some horrible looking GUI which the user never wants to see again?
So, if you are going to use native GUI for LE3, make sure there is also an option to use LE3's custom GUI and/or make LE3 skinnable via some XML file.