Jokingly, the theory is that they draw up a list of arbitrary cliche traits typically associated with defensive jobs, then they throw dice to determine the exact values.
Seriously, they probably base it off of the plans they have for future content. Keep in mind that they not only calculate our defensive capabilities, but also the offensive capabilities of the enemies we face. So, in theory, they know how much or how little defense we'll need to run into content like savage Alexander, for example. Using those values, it becomes a math equation. They basically theory craft, or calculate, what stats we would need to deal with their projected scenarios, then they would probably do some testing within the master copy of the game. If the stats don't add up, they re-spec accordingly until they have the correct values.
Parry is tricky, because it traditionally under-performs in all content. SE has been grudgingly resistant to acknowledge that in the past and continues to give it to us on all our gear. An optimistic person would probably assume that they continue to do that because they have a "plan" for making Parry viable. That's a fair assumption because they have gone on record saying, rather vaguely, that they will make adjustments to that stat. That said, it wouldn't be the first time SE dragged their feet on an issue. The fact that almost ALL of the current gear has parry on it would seem to imply that change will be soon (either just before or just after 4.0), but I'm not gonna hold my breath on that.
It's also worth noting that the best stats are typically found on Savage level gear, regardless of job or stat. SE is aware that Parry is widely considered to be the less favourable option, so it would make sense for them to put it on the gear below savage level to both reward the most extreme players in the game, as well as encourage more of us to attempt savage level content.

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