The Mark Hunt involving the killing of a "pet" Malboro named Carrot is also a reference cause it was a dispatch mission in FFT and an actual mission in FFTA.

Also, if memory serves me correct the region of Ivalice that Archades is in is called Valendia which is the name of the region where Vagrant Story took place. The Kiltia religion in XII is also the same religion the heretics practiced in Lea Monde in VS