I'm on El Cap 10.11.3 on an Early 2011 MBP with a 1Tb SSD drive.
Choppy mouse pointer from the track pad or a bluetooth mouse when on battery. Fine on power supply.
None of the efforts in any of the million threads on this topic have fixed it... except: SAFE MODE! Which means it's something third party, unless I miss the purpose of the mode. How can I get a list of everything running in each mode to send through DIFF? Or just a list of non-apple-y things?
System 7-9 was so much easier troubleshooting these types of problems, just halving the Extensions folder until the problem went away. Now stuff is everywhere rather than a single repository. Some days I miss the old pre X days... although, they sucked more often, necessitating a simpler troubleshooting mechanism.