They can be, when a process is used that has the additional diffusion steps (which was a challenge in early processes, see above).
It's very ordinary when it comes to e.g. CMOS, where the Pch has an additional diffusion to isolate it from the substrate, and the rest looks pretty normal. (Because of the additional diffusion, but also due to the electrical properties of Pch transistors, the area taken up is about double that of the companion Nch transistor(s).)
A similar process I think is used in complementary bipolar fab. Like CMOS, it just came along later, and cost a bit more to run.
As for electrical properties, proper (non-lateral) PNPs tend to perform well, but still a little inferior to NPNs: due to the additional doping steps, the impurity level is higher, and therefore they tend to have higher recombination current (making hFE poor at low currents), breakdown voltage, and fT (the upside to recombination). So there is still a preference for NPN.
You could flip the whole die, using n- substrate and having better quality PNPs and poorer NPNs, but the performance still isn't as good, because PNPs have to deal with holes preferentially over electrons. The difference is slight, compared to the 2.5x difference between MOSFETs, but it's still there. This extends all the way to single transistors (which are constructed on whatever substrate is appropriate), which is why NPNs are still preferred with discretes.
Tim