I know a few people who put the sub under the passenger foot well. they build a little box for it and it doesn't take too much room away. I find it funny people upgrade teh speakers I upgraded the amp and head unit and found out the speakers are fine they just weren't getting enough power. Yes new speaker would help with some of low end more but factory one work great if they get power. I too am looking for a place to put a nice sub but I need my trunk space.
BTW before I had the heating problem in my trunk I made a little self to stick my computer on were the CD changer would go. worked nicely too until summer came
Currently my setup is in the works again hope to put it under the passenger seat I think I have the room after I get past the power seat motors. I know people who put bass shakers there so there must be some room.