Hi zzzzzhou,
I did eventually get confirmation from my board supplier and from Intel that the xHCI controller has a limit of 96 endpoints. This limit is in the xHCI controller itself and hence there is no workaround. It is not a driver limitation or a BIOS limitation or an operating system limitation.
I was evaluating a board with an Intel BayTrail processor that has only a single xHCI controller. Hence this limitation meant that I could not use the BayTrail processor in my project. I was pretty annoyed by this limitation as there was no published documentation that stated this limitation - in fact the Intel xHCI datasheet implies a limit of 255 endpoints, but this is not true. I spent a considerable amount of time investigating this issue, and was told on a number of occasions by my board supplier that there was no such limitation, until eventually they had confirmation from Intel that the limit was 96 endpoints.
It seems that this limitation is one of the reasons why on some of the more powerful processors Intel have introduced multiple USB controllers.
Also note that this limitation does not exist on eHCI controllers.
Regards,
dh29