I have the 16-46pci and I know TV and Ron can give us comparisons from a technical aspect. But what I'm curious about is real world comparions in everyday settings.
A friend of mine has an SVS 20-39PC and I have the 16-46PC. My sub has the new, improved standard driver installed, but when I first got it, it was just the original driver. I know it's not exactly what you're looking for in a comparison, but perhaps I can give you a good idea of what to expect from the PCi models, since they're very similar in many regards.
Basically both subs are awesome. The 16-46 goes deeper, but the 20-39 just has a little more punch to it. You tend to feel bass hits in the air more with it. If you like hard-hitting techno music, the 20-39 model would probably suit your needs better. That's not to say that the 16-46 model can't hold it's own in that regard. It's just a bit smoother and easier on the ears.