My Mac (early 2008) running El Capitain has become very slow on start up & opening up aps. Once oopen it all runs fine. I am aware of clean up stuff but simply get confused with all the options available. I have never reset back to factory settings or done a restore from Time Machine however I am aware of odd & unused stuff. Most of my data is stored on external drives & use these for Working,TM & a seperate archive drive.
You might want to go to:
http://scsc-online.com/How-To.html
and read the article on drive problems, particularly the sections on system problems and user problems.
If I have external drives connected to my system during boot, it will take almost 30 seconds longer. During boot the system has to parse the drives and the externals are often asleep, so I have to not only wait for them to spin up, then the system needs to read them.
After booted, the system kicks off an mds session to index drives and it's CPU and memory intensive, lasting often several minutes. If a new drive or drive that hasn't been connected before (or in a long time) mds may re-index the entire drive, which will definitely slow you down.
Because of age it may be, as the other poster stated, the hard drive itself, but I'd be inclined to blame El Capitan first. FYI, even with an SSD, if I have externals connected, it still slows the boot time down considerably.