Sucks to lose all your storage, though. I'll bet a creative stereo guy could put a sub somewhere inobtrusive, like maybe in the storage compartment. I put my amps on a panel that I mounted on the right side of the compartment that goes from the top to the bottom of the compartment. A 12" free air sub would probably fit right in there, and take up no space. Ditto on the rattleproofing of that compartment door and the cupholders.
I don't have any experience with free air subwoofers, my sub is a cheap 10" one in a sealed enclosure. It is loud enough.
I use that compartment a lot and put my extra battery in there and all my amps and stuff without losing one square inch of storage. There is room if you are creative.