Several MIDI over USB Device
What's wrong with 16 commercial USB-MIDI interfaces and some USB hubs?

Sure, you can do this with an FPGA, but I'm not sure it makes sense to reinvent the wheel.  The problem, at least in my mind, is not so much bringing in 16 different MIDI streams so much as the interface to get that onto a PC and in to whatever software sits at the other end.  If you are doing something totally custom then maybe this isn't a major issue.  However, if you want to bring the MIDI data into a complex piece of software that someone else wrote, it makes sense to use an interface that the software supports "out of the box".  In the case of a commercial software program, this is likely your only option.  This means that you have to pick some existing protocol/interface, and build something that can interface with that.  Which is probably much easier said than done.