The fundamental difference between NPNs and PNPs is the majority carrier. In NPNs, electrons are the majority carrier, i.e. electrons are what flows from emitter to collector, constituting current flow. In PNPs, holes, which are spaces in the semiconductor lattice that are available for electrons to occupy, are the majority carrier. For some reason, which I may have known at one time, electron mobility is about twice that of hole mobility. I'm not sure of all the implications of this, but the bottom line is that NPNs are generally of higher "quality" than PNPs. This is especially true at high frequencies. I suspect you will never find circuits which operate in the tens of gigahertz range made with PNPs.
If there are any semiconductor physicists in the audience, help me out. I'm in over my head here!