SJetski,
I'd say it's several things, the driver probably being the biggest factor. When I ordered the 12", I received the old-style, but it was damaged in shipment. One of the corners was bashed in and it was about that time that the new style was released, so when I called into PE, they said I'd be getting the new style in the mail. Well, six weeks went by before I got the new sub, and when I tested them both side by side, the new sub sounded flat and dull - it didn't have nearly as much "oomph" and just sounded thin. I pulled both of the subs apart to compare everything, and the new driver was much smaller, with a thinner cone and MUCH thinner surround. The cabinet wasn't as thick and didn't have as much bracing. The amp appeared to be mostly the same. The new ports are not flared, and were actually made of cardboard instead of plastic (not a big deal, I suppose). All in all, the new sub wasn't as nice as the old sub, and it just felt and sounded cheaper.
I tried several locations in the room to see if it was any sort of room effect and couldn't make it sound any better - and I did direct comparisons with some movie scenes as well as some frequency sweeps - the old sub simply sounded better in every case.
Oh yeah, I did put the old driver in the new cabinet - it helped, but didn't make it sound like the old one - that is why I think it's several smaller issues that add up...
All that said, I still think Dayton makes the best subs for the money....