Interesting--this is the first time I've seen someone assert the potential power of the Samurai UU. Usually most people comment on how Praetorians, Redcoats, and Cossacks are overpowered, but not the Samurai. As you mentioned, few people seem to play as Japan--but I don't think that's why the power of the Samurai UU seems to have been overlooked.
The biggest problem with the Samurai is that they don't have a significant strength bonus. The Praetorians and Cossacks have a +3 strength bonus over the unit they replace, the Redcoats +2. The Cossacks and Redcoats also get an additional opposing-unit-specific bonus (Cossacks +50% versus mounted units, Redcoats +25% versus gunpowder units). The aggressive trait's free combat promotion for Samurai only works out to a +0.8 strength bonus, and that's easily matched or beaten by units produced in cities with barracks. First strikes are nice, but not nearly as powerful or important as overall strength in my experience.
In addition, as with all things, timing is everything. The Praetorians are available quite early and have a long period of usefulness (or perhaps "domination" is a better word). The Redcoats and Cossacks show up in mid-game, but are very powerful compared to both their predecessors and contemporaries, and even stand up well against their immediate successors, especially with promotions. Samurai, however, become available in the medieval era, when you're likely facing fortified longbowmen with city garrison promotions rather than mere archers in opposing cities, and more powerful knights instead of weaker horse archers out in the field. And they're quickly outclassed. Even a lowly musketman is, technically, more powerful than a Samurai.
I think you'd have to rely on the CS Slingshot to get Samurai as early as possible to make the most of them. And if you're playing at Prince or higher, the CS Slingshot is tactic with a very unlikely chance of success.