To make Intellipoint and the Microsoft Mouse prefpane work in El Capitan, you don't have to disable System Integration Protection (SIP) entirely. You only have to disable one aspect of it. Here are the steps:
1. Restart your Mac.
2. Hold Command-R until the Apple logo appears.
3. From the Utilities menu, select Terminal.
4. In the Terminal window, type this:
csrutil enable --without debug
5. Press Enter/Return. This turns off the part of SIP that will let you run Intellipoint.
6. Type reboot and press Enter/Return to restart your Mac.
7. After the restart you can install Intellipoint. Restart again once you do, and you're set.
UPDATE: dbonneville reported on 10/05/15 that you may need to unplug your mouse and then plug it back in. You may also need to plug it directly into your Mac if you are not already doing that.
If it still doesn't work, follow steps 1-7 again, and this time in step 4, run this command instead:
csrutil disable
If it still doesn't work even after unplugging and replugging your mouse, I would reenable that option with this command:
csrutil enable
I personally only use IntelliPoint for the "IntelliPoint pointer speed" which feels perfect to me, and also the ability to change the wheel button to "Magnify" so I can just press it once to zoom in and then again to zoom back out.