Even though the software is the same, The extra processors in the 1Dx make the AF system much faster at aquiring and holding focus on moving targets. This is what makes the 1Dx more expensive but also the best action/sports/BIF camera on the market. I have a 5Dmk3 as well and the difference is significant.
If you havent experienced what the 61 point AF system can do and think its overkill, dont bother as you wont read the manual to take advantage of it anyway. Ill just say that Canon has given us an amazing system and my hit rate for action has gone through the roof. The fps is an obvious difference too. Weather sealing is another factor. After a season of storm chasing I'm still blowing dirt out of my 5d mk3. The 1Dx is clean.
Low light high ISO is similar but definitely better on the 1Dx. Colors remain truer as ISO goes up.
Worth every penny if you've got the means.