Firstly, you can not use Tetra Master (FFIX’s card game, which makes a comeback for this) on the 360, but you can on the PC and PS2 versions.
You are also limited to being able to take only 100 screenshots on the 360, while for the PC you can take more (I’m unsure as to the exact amount though. I’ve heard of some image capture programs you can use, without using the screen capture with FFXI, but haven’t seen much of them tbh).
There are some other differences, but when you get down to it, the 360 version is just the same as the PC. All that should determine which one is best for you, is your own personal preference : Do you prefer 360? or do you prefer PC?