I have owned both and currently have the 306/200. In my opinion, the sound signature is different with the 306 being more detailed and neutral. I found the 303 to be more forgiven with a lusher midrange, but at the expense of a little accuracy. For me, the 303 main issue was the upper-end was a bit rolled off and smeared for my taste. This was noticeable in comparison with the Ayre CX-7.
Overall, I like both players, but would opt for the 306. I feel the 303 probably works better in less forgiven surroundings. The 303 is also a better bargain.