The problem is, they put the software that knows how to communicate with the cubes, on an encrypted chip sitting on the controller board. Most ASICs (not just miners) have controllers that communicate with the hardware much faster than a computer's available bus will allow.
Having the controller not be part of the host allows the titans to be independent and their efficiently won't be reliant on the host computer (raspberry pi in this case). The controller is definitely needed when dealing with these kinds of things.
If you compare and contrast with the BFL monarchs, they directly connect to your host PC, but rely on modified BFGminer binaries.
Each cube needs more bandwidth to the controller than USB 2.0 could provide to a PC? I'm surprised.
So, I'm ignorant about this but... Is there no way to attack the FPGA to figure out how to communicate with the cubes? I had a EE friend of mine explain to me how hard it would be to sniff the signals off the ribbon cable and reverse engineer it. He said it would be much better to try and reverse engineer the software.
I really, really, seriously, doubt that a cube would be too much even for USB 1.0.