It's much easier to change tickets on 12306 than on CTrip, The Chinese 12306 also lets you waitlist, the English version does not.
One advantage of using CTrip is that it sometimes lets you buy not 100% kosher things... e.g. I had to go from Tianjin to Beijing last week, and the earlier train that I wanted to get on was sold out to BJ but not to the intermediate stop between TJ and BJ. CTrip suggested I buy that one-stop ticket and then pay the difference at the terminal (discouraged, but generally ok if the train is not overcrowded).

Sometimes it also lets you buy 2-3-4 tix on a sold-out train, where you have to switch seats 2-3-4 times but gets you to the destination. Especially helpful when the fast trains (3 vs 4.5h) sell out for direct tickets. You can, of course, buy these on 12306, but the process is easier on Ctrip where it buys all of them for you and makes changes easier too.