the major differences between the two is 1 the weight, they dropped about 6-8lbs? and the gear box. for some reason the yamaha (and even the KTM 125) went with a 5spd gear box. it wasnt bad or a deal breaker as the engine was still awesome and could be somewhat fixed with a bigger rear sproket. also the susp wasnt as good as the new SSS forks.
overall if your looking for somethin to play on and even race. you cant go wrong with older yz's including 00-01 bikes were pretty good and these have 6spd. the thing about the bikes from the last 10-15 yrs is they havent seen SO MUCH improvement on the chassis and engine that they couldnt be competative today. the plus side is you can find them for much cheaper. for the price of a used 07 you could buy and 03 and have money for susp and engine