So each USB controller is limited to 15 (I think) port IDs in El Capitan. By default the XHC controller has more than that in the DSDT of the H87N-WIFI (15 HS## plus 6 SSP# = 21). Note that each USB3 port requires 2 IDs, one HS## to support USB2 devices that are plugged in and one SSP# to support USB3 devices that are plugged in.
My case has 2 USB3 plugs (4 IDs), and my board backplate has 4 USB3 plugs (8 IDs) and 2 USB2 plugs (2 IDs), and the board has a USB2 port for the Bluetooth on the half-mini PCIe card (1 ID). So I require 4 + 8 + 2 + 1 = 15, so XHC has just enough capacity. My DSDT maps exactly the set of functional port IDs and drops the rest.
If your case has an extra USB2 port, the same approach won't work for you (because you need 16 IDs but only have room for 15). You'd have to choose one USB2 port to be non-functional, or one USB3 port to only work with USB2 devices, or whatever.
Another approach is to remap all USB2 ports to a different USB controller (EHC1, or whatever your DSDT declares it has). That would put all the SS## ports on EHC1 and the SSP# ports on XHC, and then they each have enough capacity.
I don't think that's as straightforward as it sounds, but that's the kind of stuff people are discussing in the "get USB working in El Capitan" threads. If you want to follow up on this, you should take the discussion there.
