I'm using MS Desktop 3000 and I also became angry when I noticed that it was not compatible with El Capitan. But I found the solution. I switched to a 3rd party software. Try USB Overdrive http://www.usboverdrive.com/. It's a shareware and is free forever. The only limitation is a popup notifcation to upgrade when you start your computer.
I havent upgraded yet but it's something that I will consider if MS didn't solve the issue.
And the good thing about USB Overdrive is that.. it was able to customize buttons that IntelliType didn't allow me to.. For example, now I can customize Number Lock Key (on the number keypad), Insert Button, and everything else. The only problem is.. it was not able to detect 5 special hotkeys. Otherwise, it's just perfect.
Good luck!