Here's my idea, if ninjas are to be implemented in the game, the devs should make it so that it does increased damage to generals. If they make ninjas into a merc, then make the troop size 1 and cost a lot of trade goods. If ninjas are an actual unit, then the devs should create a whole new class of unit, the spy whose goal is to kill the general, as usually that's their goal in the battlefield and that they are usually invisible to defenders/defense unless spotted by a tower. From this the Japanese will get the spy who has some unique trait, maybe quicker speed or something.
In order to prevent people from being like "why should I even get a general then", nexon should improve the generals by giving them Rise of Nation type mechanics, where troops within their sphere of influence gain bonus attack, defense, speed etc and the generals can get special abilities like in Rise of Nation that enhance the battlefield. That way generals are more of a threat for which spies can be used to counter.
Moreover, maybe the way people can get spies/ninjas is by building a specific building available during either the\ medieval era that allows recruitment of spies or produces a lone spy as defense against generals. In order to counter spies while on the offense, players can use the supply cart which provides vision of the spy. Therefore, supply carts are even more useful and not only do they heal but provide defense against spies.
Just my idea, what do you guys think