How to activate all USB Ports in El Capitan 10.11.4

Hi Sofista,

I put your question into the proper section.

Do you have a DSDT? Do you use a kext like USBInjectAll?

Under the assumption that we talk motherboard, not USB PCI cards, IMHO the best approach is to use USBInjectAll.
This will inject a number of USB Ports depending on USB Chipset and/or Mac model.
Not have all of those ports might be accessible on your board.
This can be remedied by creating a custom SSDT, which allows you to select the ports you want to have injected.
There will be a limit of 15 ports added regardless of SSDT or not. USB 3.0 ports occupying two slots, one as USB 2.0 and one as USB 3.0 port.
In the case you need more than 15 ports you can add a patch to increase the number of ports allowed. This might cause problems though. But if and when nobody can tell.

At the moment USBInjectAll does not support USB3.1 ports.

GenericUSBHCI supports 3.1 ports as well as USB 2.0 and 3.0 but uses a different method of detecting and injecting USB ports and is not restricted by the 15 ports limit, but behaves in my experience erratically.
Ports might be detected or not. It might be related to the total number of USB ports including those of USB Hubs, but it really needs further investigation.

An advantage of both is that they install cleanly. You only add, you do not have to patch. If you exceed the 15 ports limit, you will have to patch, but if you are using Clover this can be done on the fly by Clover.

My personal preference is USBInjectAll with a custom SSDT.