Changes from 3.0E to 3.5E

Why change the martial artist for the revised rules? For the following reasons:

There have been comments that the class is rather bland, in terms of class abilities. Lots of bonus feats allow a high degree of customisation, but also aren't very flavoursome. Thus, changing the martial artist's abilities to give it a stronger identity wouldn't go astray. This is reinforced by how the 3.5E ranger is very similar to the martial artist (good Fort and Reflex saves, fighter BAB, light armour, lots of skill points), so there may be a need for differentiation.
There have also been comments that the class is too powerful. Personally I think the problems are exaggerated, and playtesting hasn't revealed any major balance issues. Certainly anyone who think a martial artist is a slot-in replacement for a tank fighter is going to be disappointed; while the class is better at kicking butt than a monk, it's still not going to survive long in toe-to-toe combat with a melee brute. Still, the class is fairly strong, and to some extent, perception is reality.
The mechanics of some class abilities have changed from 3E to 3.5E, like uncanny dodge.
A number of feats could do with rewording or rebalancing. Instinctive Shot, for example, isn't really powerful enough to justify delaying it to 6th level.
Because I get my jollies out of dicking my users around. What are you going to do if you don't like it? Stop sending me money? HAW HAW!

With these reasons in mind, the class gets the following changes:

The bonus feat at 1st level is removed, and the total number of bonus feats reduced to 8.
Starting at 10th level, the class gets a bonus to Balance, Jump and Tumble skill checks. The martial artist also gets to take 10 on these skills at any time, from 7th level.
Uncanny dodge is changed to follow the 3.5E UD/trap sense convention.
The list of martial artist-specific feats gets a makeover. Enhanced Unarmed Strike becomes class-specific, allowing the class to take over the unarmed combat niche that the monk occupies. Flurry becomes Rapid Strike, and is opened up to all classes. (The existing Rapid Strike becomes Improved Rapid Strike, with substantially different prerequisites.) Instinctive Strike and Strike Without Thought also becomes class-specific, to reduce the cheese possible when clerics take them.
Several other feats are modified; in fact, nearly all the combat-related feats are tweaked to some degree or other.

Changes from v1.0

A few changes and clarifications have been made to the original version of the martial artist:

The martial artist's starting gold is 3d4 x 10 gp.
The level-based AC bonus is now a dodge bonus, so it is lost whenever the character loses her Dex bonus to AC. It starts at +1 and increases by +1 every six levels, instead of starting at 0 and increasing every five levels.
Added Ambidexterity and Improved Initiative to the list of bonus feats.
Added an Improved Flurry feat, that mimics Improved Two-Weapon Fighting.
The Improved Arrow Deflection feat imposes a cumulative –5 penalty on deflection attempts after the first (so the second deflection attempt is at –5, the third at –10, and so on).