Building a Kensai Magus//Inspired Blade Swashbuckler. The Inspired Blade has the following capstone:
Rapier Weapon Mastery (Ex)
At 20th level, when an inspired blade threatens a critical hit with a rapier, that critical hit is automatically confirmed. Furthermore, the critical threat range increases by 1 (this increase to the critical threat range stacks with the increase from rapier training, to a total threat range of 14–20), and the critical modifier of the weapon increases by 1 (×2 becomes ×3, for example).
While the Kensai's capstone is simply the fighter's Weapon Mastery:
Weapon Mastery (Ex)
At 20th level, a fighter chooses one weapon, such as the longsword, greataxe, or longbow. Any attacks made with that weapon automatically confirm all critical threats and have their damage multiplier increased by 1 (×2 becomes ×3, for example). In addition, he cannot be disarmed while wielding a weapon of this type.
Now the confirm critical part is a simple yes/no, and since the Swashbuckler ability is 'greater', if you have to get only one you get that. But the increase in critical damage multiplier does not specify that it does not stack with similar effects. So with having both, will a level 20 swash//magus's rapier attack have a 14-20/x4 crit modifier?
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Also as an aside, if you have the half-elf's multitalented race ability, can you effectively get two favored class abilities every level with a gestalt character?
Official Pathfinder has no rules for gestalt characters, so... ask your GM.
I cannot find any rules regarding gestalt characters in Pathfinder, so I have to default to using the 3.5 rules for it.
1. They stack. It's only fair for them to, as you have spent your career wholly as two different classes mastering the same weapon.
2. Inconclusive, as favored class bonuses did not exist in 3.5. Consult your GM, but my opinion is that it's slightly strong, but not too strong.
While you have two favored classes, you only get one "point" for your favored class bonus at each level.