In many cases, El Capitan speed problems are related to the 3rd party additions installed on the older OS X release that were inherited, and are no longer playing nice.
You could post the EtreCheck output, and someone is sure to express an opinion about what is shown.
<https://discussions.apple.com/docs/DOC-6174>
<http://etrecheck.com>
NOTE: a lot of times anti-virus, Mac cleaners, and memory cleaners are at the root of many performance problems. If you have any of these, you might consider removing them.
You can also try booting in Safe mode, which does not load the 3rd party additions. If the system performance improves, you again should look at cleaning house.
You should also look at Applications -> Utilities -> Console logs and see if there are any processes that are throwing lots of messages into the log very quickly. Especially, start process, process dies, start process, process dies, start process, process dies, start process, process dies, etc... These kinds of problems do not tend to show up other places.