I get what seventy one is saying about the age of this thread, but I came here yesterday, hoping for an answer. I saw that there were recent replies, and read through the whole thing, without finding a solution. So, I'm going to post about my experience here, in the hopes that it helps someone else who stumbles upon this. And, I'll look for, or create, a new thread, about what I did.
I have a new iMac, with a Magic Mouse 2; I was so excited to see that it can be charged - my older MM is battery powered and goes through so AAs that I stopped using it. But the MM2 never worked right out of the box, AND I'm running el Capitan. Not only did it not scroll, but the mouse/trackpad/accessibility/bluetooth panes did not provide any indication that the computer knew that this was a MM2. To be specific, the computer did refer to is as "Magic Mouse 2" but the controls didn't offer the programming nuances available to the device, only the standard mouse. So, I thought maybe I had a software issue, like, perhaps, I was missing something in the system prefs. I got busy on a project and reconnected my trusty Logitech wireless mouse. But MM2 should freaking work, and it was bothering me, so I poked around again yesterday to find a solution. I did my system update (I went from 10.11.3 to 10.11.4), hoping that would help. Alas. No.
Last year, I had a lousy bluetooth keyboard and in frustration, I tossed it in the bin of electronic paraphernalia in my closet. And for no reason, it paired with my computer, from the closet, 6 months after the fact, and even though I turned it off, and clicked the disconnect button under the Bluetooth icon in the top right, nothing seemed to work. I held down the option key while clicking the Bluetooth icon, and the menu changed. I scrolled down to the bluetooth keyboard, and clicked REMOVE (not disconnect, because apparently some devices will not obey), and woohoo, the **** thing was finally banished.
So after updating my system with no change with my mouse, I did the same thing: option-clicked the Bluetooth icon, and removed the MM2 (again, do not select disconnect; use the REMOVE option). You'll likely need a backup mouse to pull this off - I reconnected my Logitech and used it to re-pair/re-discover the MM2, and -- yay! -- there it was, AND it opened up the proper mouse control, offering me all the gestures and scrolling options I know this little guy is capable of.
Sorry to ramble. But hope this helps.