Well, the biggest difference is that the Fast Track Mkii only has one mic input while the Mobile Pre has two.
I've only borrowed the Fast Track Mkii--I don't own one--but I wasn't able to notice any real difference in audio quality between it and the Mobile Pre I've owned for several years. FYI, I use the Mobile Pre with measurement microphones into SMAART for check room and system performance when setting up live sound rigs--and the quality is good enough that my measurements are accurate. Obviously I also use the Mobile Pre for location recording and am happy with the quality.