I was not aware that square taper was still offered on high end sets.
I would imagine that the outboard is a lot stiffer - I've compared Octalink, which is kind of Shimano's version of ISIS (on a flexy steel bike) and square (on a stiffer Al) taper and I definitely tell the stiffness difference which would lead me to assume that the outboard is a wayy stiffer. However, said stiffness was only felt and probably only necessary when you need to do quick starts and sprint and stuff. Unless you race and plan on dropping the hammer a lot, the outboard seem useless to me.