Generally, I agree with the OP. The non-Western/Eastern idea of an archetype is usually bound to fail. "Samurai" can and should encompass a lot of character builds -- we can easily see that kind of an archetype encompassed by Warblades, Fighters, and so on. You could focus on fighting with the daisho, charging, mysticism, and so on and so forth. So, making a class that encompasses all of that is bound to be a fools' errand. And, that's without bringing in any concerns about fetishism by the authors.
It is better, then, I think, in a system like 3E D&D to leave it to the player to figure out what their Samurai, Ninja, Mamaluke, etc. looks like.
That being said, I think game designers often use names like this as an excuse to bring in other classes or variations. If a designer wants to label his idea for a Rogue with a little more mysticism the "Ninja" or decide to label their magic-using class with some wonky spell mechanics "Sha'ir" I guess I don't really care. So long as no one puts any weight on that decision. No one I've ever played with does, but that might not be everyone's experience. After all, it's not like we didn't make knights before PHB 2.
I don't think there's any need for even class variations, really. That just seems to be adding to the problem and the confusion. One should be perfectly able to build a Samurai, etc. out of the existing materials. The game should (ideally) be nimble enough to support them.
P.S.: in a lot of ways, I guess, I agree with the idea behind Pathfinder's approach. As usual, my problem with PF is its implementation. But, I don't like loading up on variant class features/archetypes/whatever they call them. There's no difference in making a bunch of Fighter "kits" that relate to Samurai and Mamalukes and whatevers and making different base classes. Just make the Fighter class flexible and interesting enough and make feats cool and useful enough to let me play any archetype I want. That saves everyone from being pigeon-holed, so that not every Samurai has to wield a katana or a daisho, for example.