Hong,
I prefer customizable classes to stiff prestige classes corsets (CORPS lovers unite!). I consider your Martial Artists superior because of its flexibility... so, using a prestige class to portray just one style is not a concept I'd cherish. Besides, 20 levels is not going to suffice if you want to create Bruce Lee clone.
On the other hand, martial arts are all about perfection, attaining certain ideals, etc. I feel that it would be better idea to allow for tree (path/ladder/whatchumcallit) mechanic to justify the existence of grandmasters (you know, these old panty chasing hundred year old freaks) and style specialists. Chainmail Bikini Games Beyond Monks would be a good example of similar solution (there are some problems with d20 mechanics which made me skip the book). And while talent paths are not a part of standard d20, feat trees surely are - just look at Whirldwind Attack requirements.
By creating Graceful Crane Stance Mastery feat and listing a list of prerequisites ("any three of the following list") you'd reproduce the mechanic while allowing the player to choose the way he or she is going to use to achieve the feat.
This way, there is going to be a sound reason to stay in your class, and, at the same time you'd ensure that Martial Artists were unlikely to be the same.
Regards,
Ruemere
PS. One does not have to be of a ninja class in order to be called one. Personally, I'd prefer a Martial Artist with a good choice of feats and skills.
edit: corrected typos
edit: corrected publisher for Beyond Monks