While I wouldn't call blender's compositor "weak", I can see a few notable differences that would make me choose one app over the other for certain tasks.
The Color Management in blender is limited to the final output with not a lot of options for changing color spaces or other LUTs unless they are part of the config.ocio. Having Ocio operations as nodes in natron adds a lot of flexibility to deal with sources from different sources.
Blender excels at 3D (obviously) physics simulations, etc. Exporting EXR files from blender and back is the best way to make elements work on both platforms.
Tracking is way more responsive and faster in blender. The tracking interface is very well designed making it very easy to see if the trackers are sticking or slipping with a preview window. Rotoscoping using trackers is quite effective in blender.
Making masks in blender is a breeze and way more stable at the moment than natron's bezier curve editing. Getting soft edges on masks in blender is quite easy.
Natron has a lot of options when it comes to encoding, while blender's are quite limited.