The serious answer: pretty much all of a ship's stats are boosted in some way by the pilot's. Even without upgrading the ship at all, you should notice a marked difference between characters you've already farmed and characters you just got when playing ships.
All of a ships Protection comes from pilots. Also basic stats such as offense, health, and protection comes from pilots. Plus, the gear level of Pilots effects the pilot ability max level.
All of a ships Protection comes from pilots. Also basic states such as offense, health, and protection comes from pilots. Plus, the gear level of Pilots effects the pilot ability max level.
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The serious answer: pretty much all of a ship's stats are boosted in some way by the pilot's. Even without upgrading the ship at all, you should notice a marked difference between characters you've already farmed and characters you just got when playing ships.
It's all in the pilot as they say?