I'd say that the main difference is that wow has a larger pvp audience and the game was really built for pvp from the ground up, while FF is creating a PvP system bit by bit, by mostly making trials and errors, because of that PvP is not something that entices players to buy the game and is more like a side option.
That said I do think that they realized sooner than Wow that they had to split PvP and PvE to try and keep the two balanced without becoming crazy. On wow on numerous occasions PvE had some nasty changes that were born from PvP nerfs