What settings you change that are a big deal to you? I'm not talking basic stuff, stuff that made a big difference on how you use the cameras on a day by day basis.
For example, a few things I changed I think are going to make the camera much more friendly for me.
The SET button I have set to ISO, now instead of fumbling for the tiny button up top (which is harder to press now) I can just hold down the SET button and move the top wheel to change it. Just feels a lot easier.
Love the new minimum shutter speed, I have it set to 1/60 now so when I am in AV mode it never drops below that, but seriously considering just setting it to 1/125 because I mostly shoot people and that's the minimum I like to shoot at.
I have been considering turning on only cross type points for the Select-able AF points. This reduces the amount of points, but I think it will make it more reliable. I haven't had a chance to really test this theory.
First thing I did was turn off the LCD AUTO brightness, that thing drives me nuts. Initially look at your review image and it is grossly underexposed and then hit play again it is fine. Too difficult to know quickly what my exposure looks like. I do use the histogram as well. I set it to manual: 4 for now. I just don't like it changing on me when I am trying to quickly view my review image.
The multi-function lock is another one of my favorites. By default it only locks the job wheel, but you can include the quick wheel and/or the multi-controller. I have it lock both wheels, and now with the mode lock I can be assured I can lock all my settings and not worry about it changing. Mode never gave me a lot of problems but I did frequently knock either the aperture or shutter speed dials from time to time, so being able to just flip the lock switch when I know I won't be changing much is a nice change.
I changed the multi-function button (press in middle) to reset AF point to center. This is pretty useful to quickly set the af point back to center. Not much else you can use the button for.
I am using the warnings in view finder to tell me when I have a custom white balance set, the two uses I find for this (depending on what you do more) is to let you know when you are using spot metering or using custom white balance. The other options not that big of a deal. I'd love to use it for both, but it doesn't differentiate which is set. So you get a ! no matter what trigger you set. It is a fairly good size icon, they could have easily made it say CWB or SPOT so you can tell which is being flagged. Either way, minorly useful.
Those are the main changes I found I thought would be useful that actually changed how you work with the camera.
Be curious what others are doing.