I haven't heard the PB12, but I did have a Elemental Designs A3-300 for awhile (which is nearly identical in design), and I do own a couple VTF3s, so I will just comment on those. Output-wise they are pretty similar. They both had good sound quality too, although they didn't sound exactly alike, and on this point I preferred the VTF3, although the difference wasn't huge. The VTF3 handled deep bass better (in max extension mode), at high output it is not hard to get the A3 to chuff below 20 hz, from the text tones I ran. You can get the VTF3 to chuff too, but it is less audible and it has to be pushed harder to reach that point. I would expect the PB12 to handle deep bass (<20hz) slightly better than the A3 because of the slightly larger port width.
Something else I should say is that is that it was easier to achieve a good powerful bass sound with the VTF3s placement as opposed to the A3's placement. What I mean is the VTF3 seemed to sound powerful in more places in my room, whereas the A3 was pickier in placement in order to equal the VTF's loudness. But, in the right place, it could be a match for loudness and punch. In the end, I think the VTF3 is a better sub when pitted against the A3, but keep in mind the VTF3 is normally $800 shipped, and the A3 is $600 shipped, so it's not a fair comparison.
As for the major differences between the VTF and PB12, the VTF has an adjustable tuning point, where you can sacrifice overall loudness for more deep bass, and vice versa. The PB12 won't have this, but, from what I understand, it now has a some internal EQing that can be done with it's DSP amp, and also it's digital limiter can squeeze the most out of the driver without letting it bottom out. I'm sure you would like either one, I think they are both fantastic subs for the money.