the 00 gundam's ability is not yet been seen, though it is clearly seen that its a much more powerful ms compared to exia.
but I think that exia has a chance against freedom, even with s.freedom i think setsuna has a chance.
the variable phase shift is a non-factor against beam weaponry, even if the gn blades and swords can't dent the vps, i think it'll give a good whack on the sf.
dragoons are not really a factor, since setsuna has faced the gn fangs of the throne zwei, so remote weapons will not be at an advantage of the sf
setsuna will probably force this encounter to a melee battle, thanks to the trans-am, even if kira goes seed, the exia will have an advantage on speed, though it may be a different story if kira goes seed, if he can't shoot it down, why bother shooting.
but it kira gets the emogodlikecantshootmedownprotagonist plot hack armor, it a different story
though if they release a gundam g generation with 00 and seed/destiny, well have a good answer to who is better