I was thinking about it last night, and came up with a couple thoughts.
Assassinate:
Make it damn near impossible to miss with a full study.
Balance: Make study time longer.
I was trying to think of ways to make this balance out well, and it took me a while, considering how powerful assassinate really is.
Ninjas are supposed to be assassins, masters of the blade, but they aren't samurai. IMO a ninja should be able to kill anyone, without a godset because of the time and energy it takes to get a study.
Dunno how people are gonna feel about this but I say you take some of the melee vitality from ninjas, make assassinate more likely to succeed, and add encumberance to balance.
Since when does anyone remember a ninja running around in platemail? Can't imagine it's too easy to jump out of the shadows with 80lbs of chainmail on..
(Sorry this is so scattered, you get the point though)
