Keep in mind the issue is not upgrading the game, but alienating the client base.

Shutting down support for a PS2 version of the game would removing some players only means of playing the game and result in a loss of players and revenue (how much depends on the figures of course).

Performing a system-wide graphics upgrade after the PS2 is removed would jeopardize many current PC players. This game runs on practically any computer right now and that's a huge benefit. You cannot simply look at PS2 vs PC player stats - you would need to know how many people play the game on net-top boxes (ITX systems and even atom/ion systems run FFXI perfectly and are a more affordable solution than a new rig or auction-purchasing a PS2), how many play the game through virtual machines (linux/mac), how many people play the game on older laptops or desktops that can't even power a new graphics card.

A graphics upgrade would be nice, for sure, but think of it this way... how many "general" computer users would be upset if Microsoft came out and upgraded MineSweeper (on all versions of windows) to an all-out HD awesomeness game that only a 16 core, 48gb RAM, latest gen graphics card could handle?

If you place consumers in a position where they must upgrade a system to continue playing a game they have been able to play for 9 years, they are either going to quit playing or they will upgrade their system and start playing newer games. It's an overall loss to the player base in any real analysis and that's devastating to MMOs.