I'm in the process of switching over myself (Canon 6D -> Nikon D750). I would say the biggest challenge is the ergonomics of the Nikon. After shooting with Canon DSLRs for so many years, Nikon's button layout just feels wrong. I have something of a laundry list of design gripes specifically with the Nikon D750, here's a couple off the top of my head:
1. Nikon's front dial is further down the grip than on Canons, which makes it harder to reach.
2. The default ISO button is on the left-side of the camera which means you can't change ISO with one hand. This can be partially fixed by remapping it to the record button. Also the screen lights up every time you want to change ISO (why Nikon?)
3. The menus feel unintuitive, but maybe it's just habit. It takes a lot of button presses to do something like change the flash power of an off-camera flash. The menu lag is real however, it takes roughly 3 sec to bring up the menu from sleep mode.
4. Wifi functionality is rudimentary. You cannot change exposure using the mobile app, only focus and shoot.
5. The build quality feels flimsier than a Canon prosumer DSLR, there is a lot more plastic in it's construction.
6. AF points are all concentrated in the middle of the frame, which prevents you from being able to focus on details outside of the middle. It will also cause the Nikon to miss focus on moving subjects more often than a camera like the 5D3.
Despite all of it's shortcomings, the image quality and dynamic range of the Nikon is superior to the Canon so I can tolerate it being a more fiddly camera to operate.