JR here is another option for the square hole in a rounded surface problem. Wait until after you smooth the surface. Then cut the hole and bevel the edges.

No odd pinching in the corners with this mothod. But I think you'd have to delete history and uv layout the more dense smoothed model.

note 2.

Also your leading edge at the root is quite squared off and should be rounded.

Once again I think this problem can be fixed if you look at the way this filleted area of the wing is constructed in the actual airplane. Its really a seperate piece, so you might want to consider using a nurbs surface fillet to recreate it.

Make the fusalage, the wing and the wing fillet seperate parts. This way you could keep the wing and fusalage geometry lighter and take advantage of the nurbs surfacing fillet tool to create that shape.