El Capitan and Microsoft Mouse (IntelliPoint) Not Working

I found a kind-of/cheap fix.

Uninstall the prefpanes for Intellitype & Intellipoint- they don't do anything at this point, and can interfere with the base system behavior in a negative way.

Open System Preferences > Keyboard > Modifier Keys

Select your keyboard, and swap Option and Command.

Unfortunately, to get smart keys back or extra buttons on the mouse, a piece of 3rd party software like better touch tool is needed.

I had switched to MS ARC Mouse after my hands started having severe pain with Apple MM. ARC had worked with all features in Yosemite but I had to include MicrosoftMouseHelper application in Login Items.

After upgrade to El Capitan it works as standard mouse only. I could install Intellipoint software by allowing it in System Preferences / Security & Privacy while it installed. Then I came across this thread and tried all these but no luck. Intellipoint is getting installed without any issue always with changes in Terminal or without it but Back button and centre wheel button do not work. I even included  MicrosoftMouseHelper in Login Items as before. No luck.

Tried installing Bettertouch Tool but is not quite user friendly like MS Intellipoint.

Problem solved:

The problem I encountered with SteerMouse is the terminology used its control panel interface.  When you set "Primary Click", you'd expect this to mean a normal, simple click of a mouse button, but no.  This apparently only happens with "Secondary Click".  When I gave then left and right mouse buttons the "Secondary Click" option, then they finally started functioning properly. 

However, one of your mouse buttons must be given the "Primary Click" option -- SteerMouse insists on this because it assumes you will not have a functioning mouse if none of your buttons are set to "Primary Click".  I chose to give the "Primary Click" option to the scroll wheel as I have never used the click option on the scroll wheel before. 

So long story short, giving "Secondary Click" options to both left and right mouse buttons gave me back my mouse.

This is not entirely true because my mouse no longer can change tool features in Abobe Illustrator with one click.  I now have to toggle the Option Key and Mouse and the click-scroll through each tool to get the tool I am looking for.  This feels like an odd hoop to have to jump through, and a tad bit annoying, but I think I can start doing it quickly and easily with a bit of practice.  At least I have my IntelliMouse back, that is a big deal... at least until OSX10.12 comes out.

I also have this problem.  While I can switch back and forth between Windows and Mac and not have keys trip me up, having the Command & Option keys in the wrong place really messes me up.  Missing my fourth and fifth keys on the mouse is annoying as well.  My wireless desktop keyboard is one of the best I've ever owned, same for my Intellimouse.  It makes me a bit sad that they've been kneecapped.

I tried USB Overdrive and that just makes my mouse unusable.  Neither left nor right click will work no matter what I set them to.  SteerMouse is a bit better, but it just gives me exactly what OSX 10.11.1 gives me.  Left click doesn't function, only right click works, but I have never used right click so trying to work with right click after having used left click for the last 25 years is a pain and causing me some productivity loss.  Oddly, when I bring up the SteerMouse control panel, left mouse click works fine, but as soon as I close the SteerMouse control panel, left click ceases to function.  Its the same when I boot up my computer.  I can left click to enter my password, that is fine, but as soon as my iMac boots up and I am passed sign in, left click stops functioning.  I hope someone will create a usable non-Mac mouse, other than the traditional Mac Mouse that works with OSX 10.11 and higher.  I find the magic mouse a pain to use.