I've been playing the PC version for about 4 months. I did go ahead and pick up the PS2 version.
Here's a quick pro/con .
PS2:
Cheaper Version
Play on TV
Does Not Lock Out Computer
Game is more expensive
PC:
More Expensive If You Need Hardware
Easy Keyboard and Controller Support
Game Is Cheaper
PC Locked - (When playing FFXI, you can not get back to windows or minimize the game without logging out, if you do it will force log you out, this was done to prevent cheating).
NOTE: This lock out reason is why I got the PS2 version, so when I want to I can play the PS2 version and still be able to acess stuff on my PC. Anyone else thinking of getting both, I do have to congratulate Square, using existing PC account on the PS2 version was very very easy to do.
The BIGGEST difference in the two is graphics, and it is a BIG difference.
The PS2 version, to be blunt, looks horrible. The lowest settings on the PC look a little better. In video's you see names above characters and enemies, in the PS2 version, they are there, but you CAN NOT read them unless you select them, and see the name in the corner of the screen, or you get very very close to them. It's sad because if you do have a PC that can max out FFXI, you are presented with an absolutly beautiful game.