That's a damn hard question. FFXI's end game system requires a change from guilds imo and linkshells were perfect. But guilds meant committing to one group of people and as such your bad nature(if you had it) was suppressed more commonly. In other words guilds were like jobs or family(more permanent) while linkshells are more like part time(short term) Guilds were an investment and while it didn't keep everyone in check, the system was needed to hold a group together through a tier system for end game.

People like to talk real big about FFXI and it being for the hardcore player, but in reality the game is designed for casual gamers big time. SE simply dropped the ball and miscalculated the grind for their goals. It's very tame in requirements for doing end game. In the "other" system which there is basically only two systems -FFXI and EQ- it absolutely requires you have done 8 tiers of end game for the right gear to have a chance in hell at defeating tier 9 content. You simply cannot accomplish such a task through means of pick ups and jumping around constantly amongst linkshells. You can try to your hearts content but it really is a lost cause.

Both systems have their advantages and disadvantages. But overall I think I like guilds better. They provide a lot more control and leadership structure. But they have no need for here. A little bit more work put into linkshell functionality would have been nice, though.