"If I clean install El Capitan again, will the speed be faster than now in general?"
It might become -a little- faster.
But honestly, probably not going to increase speed that much.
Questions:
What kind of drive is inside the Mini?
Is it the original, platter-based hard drive?
If so -- that's what's slowing things down, and there's not really much you can do to speed it up -- other than perhaps replace the drive with an SSD.
El Capitan just "runs slower" on platter-based drives than did old versions of the OS.
Again, the only real solution is to use an SSD instead.