I stand by my initial analysis, but allow me to expound a bit:
At it's core, Susanoo'O is a fire tech.
RasenShuriken is a wind technique that transforms the compressed spinning chakra into spinning compressed air.
Rasengen Shuriken is a wind technique.
As stated in the manga when Naruto first learned how to do elemental release, Fire tech's are strong against wind techniques and weak against water.
It's not been specified in the manga if earth and lightning techniques have any particular weaknesses or strengths against fire techniques, but i believe it has been stated in some of the video games. That's a strict non-canon interpretation, but it does fit with traditional chinsese elements (Lightning can stand in for metal in some instances of chinese medicine), and probably makes for good game balance in some situations.
As a wind technique, it would make sense that Susanoo'O is strong as a defense against RasenShuriken as it should cause the Susanoo'O user to be surrounded with enhanced flame that becomes non-existent within the center of Susanoo'O, while immolating the things on the outside of Susanoo'O, but Kishi sometimes forgets small things like that for the sake of the story.
I can speculate about yin and yang elements and how they differ and a bunch of other stuff that is fairly tangent to this actual thread, but as far as Susanoo'O vs RasenShuriken goes all that really matters is fire vs wind.