I had the same problem, USB debugging enabled, device showing up in windows but I never got the question about RSA fingerprint when I connected my Nexus (6) device, nor did it show up in the Android Device Manager.
BUT In the windows device manager I did have an entry saying it was an android device and Composite ADB interface etc. Still didn't work. When I tried the previous tips about manually updating the drivers, Windows 8.1 just responded that "Windows has determined that the driver software for your device is up to date" this was not true. Looking at the driver details I saw that the driver was published by "ClockworkMod". I realized this must be because I had installed the Helium app sometime last year. So I uninstalled that, still had the same problem. Checked again, this time it was indeed google drivers, but version 7 published in 2012 (and not version 11 published 2014). I uninstalled these AS WELL and then tried the trick of reinstalling the driver from the SDK located in: %localappdata%\Android\sdk\extras\google\usb_driver
Now when I replugged my device it finally works and can be debugged with Android Studio. Indeed a driver problem.