I just downloaded Adobe Creative Suite 6 Master Collection on my new 27" iMac.
Every program in the suite installed properly with the exception of InDesign and After Effects.
InDesign gives me this error message: You can’t open the application “Adobe InDesign CS6” because PowerPC applications are no longer supported.
After Effects gives me this error message: You can’t use this version of the application “Adobe After Effects CS6” with this version of OS X. You have “Adobe After Effects CS6” 11.0.
I downloaded CS6 using this link - Download Adobe Creative Suite 6 applications - and then selected CS6 Master Collection, put in my serial number and went along my way. Like I mentioned, everything downloaded and installed fine with the exception of InDesign and After Effects.
CS6 is unsupported under El Capitan. Unfortunately you are on your own here.