For one, it has a true threshold based all-metal mode with VSat which can be turned into a static all-metal mode (and iron 'grunt'). 2nd, it has a mixed-mode relic mode with VSat in the all-metal channel. 3rd, it has true ground tracking which is also, AFAIK, the best in the industry. (also has a salt tracking mode, though I've never used it) 4th, it has variable target reject volume (which I utilize on mine and is useful in trashy areas). 5th, a threshold based coin/relic/all-metal mode with a user adjustable threshold. 6th, more tone options (up to 22, though I generally like

. 7th, a volume control. 8th, VCO on/off . 9th, retains settings in ALL modes when turned off, not just custom mode as in the AT Pro. 10th, variable intensity backlight. 11th, a locking pinpoint mode. 12th, a faster target recovery speed. 13th, the ability to find considerably smaller targets (great for prospecting).
The AT Pro DOES allow for manual ground balancing, which the MX Pro doesn't, and has a bit more resolution in the iron range. The standard mode can be considered a non-VCO mode, but it also has a slower recovery speed. The MXS recovery speed isn't affected by VCO on/off.