Not a Mixtrack user, so this is just based on what I’ve read. As I understand it, the controller ships with DJ Intro rather than the full version of Serato, and not all the functions map to the Mixtrack – you have to upgrade. Perhaps this is the problem you are experiencing. Also, depending on the amount of time/effort you want to put in, you could download a demo version of Tractor Pro, a map for the controller (http://www.traktorbible.com/freaks/mappingview.aspx?id=639) and give it a go.
General consensus seems to be Serato is easier to use, better for scratching, Traktor allows for more creativity (and is said to be the choice of pros, whatever that means). Agree with djrizki – what’s comfortable to you is what’s best.
But no matter which you choose, you will want to upgrade to the full version.