Qualcomm looks like a beleaguered company. Hardly a week goes by without another government probe, legal attack or other setback. In the past couple of weeks, it has paid a settlement fee to Qualcomm, continued to up the ante in its litigation with Apple (an important customer which may be slipping away to Intel and others), and faced possible challenges to its highly strategic acquisition of NXP. But amid all these difficulties, Qualcomm continues to hurl out the innovations. It is likely that it will be forced to make significant changes to its business models, its licensing practices and its scale of royalties in the coming few years. Those may lead to a Qualcomm with a very different level of…