Interesting. I see lots of comments like this. I personally look at what is portrayed mechanically before I pay attention to the cultural trappings.
I personally think the Samurai (The OA/Rokugan one, not that complete warrior abortion) does a wonderfull job of portraying what the aristocracy in a DnD world should actually look like. Strong will save, 4 skill points per level and a skill list that would allow one to learn to become an effective govenor or general. Dump the Ancestral Daisho for a Lance and Longsword and swap out the feat list and you can portray Lancelot or Arthur or Prince Henry far better than a fighter or the NPC classes can. The fighter make for an awful leader thanks to his abysmal skill list, and the NPC classes don't allow for people who are as effective as DnD nobles would have to be. Of course that fact that the Samurai is in fact supposed to portray a feudal aristocrat explains this, neh?
As for the ninja I think he makes a pretty damm cool fantasy assasin regaurdless of the cultural trappings you want to dress him in. Give him necromantic trappings and you have an assasin who studies incorporal undead to gain creepy skills. Or turn that around and make a profession of ghost hunters, since ninjas are about the only class that can reliably whomp on incorporeal undead at low levels.
All you have to do is change the names and I think these are great classes for any feudal fantasy settings.