I don't really know what the gen2 sub setup is like.. but a lot of factory systems use weird impedance subs (3 or 6 ohm) which you can get around.. on top of that they are made for the tiny enclosures that the OEM builds. After-market subs generally are 2 or 4 ohms (other exist I said generally)
So with all that said, if you can find out the impedance of the factory setup, and measure the factory box size you might be able to find a suitable direct replacement, but it's unlikely to sound much better or be any louder.
If you want to replace the sub and the enclosure, then you have some more options, but I doubt the factory amp puts out much power so I doubt it would be a huge improvement there also...