here's my adventure in replacing the sub in my 99 gs300 that may be helpful in getting the sound you want...
i first replaced the factory sub with a jl in my '99 first. it sounded much better and i got better bass out of it, but it wasn't satisfactory. one problem is the gs audio system sounds damn good (coming from a car audio enthusiast that used to spend thousands on car audio), but it also has built in "bass control" and it lowers your bass at higher volumes to protect the sub. so when you turn it up your sub will never be as loud proportionately at higher volume. also, i listen to all kinds of music from jazz, rock, pop, rap, electronica, and everything in between and the biggest problem i have is being able to control the amount of bass/boom for a specific type of music.
in the end the the solution came in a 12" solobaric kicker sub in it's own enclosure, with the original sub taken out to allow for air movement to the cabin, to help feel the bass. there are plenty of other subs out there, but this one has a dual coil and according to my installer acts almost as two subs in this fashion and is convenient for saving space. a viper amp in the trunk, with separate volume control mounted under the dash, so i can easily control sub volume according to the type of music.
i couldn't be happier for several reasons. one, it sounds great. two, it's not permanent and can easily be put back to stock and taken out. that way, when i can get my new 06 gs it will go in there. three, the separate sub volume is a must for correct sound control, as i listen to all kinds of music and take 5 from dave brubeck wouldn't sound very good with the sub set for a pounding trance song from dj tiesto. four, the sub enclosure fits great on the trunk "shelf" against the rear seats and takes up minimal trunk space. lastly, it wasn't that expensive to round out the sound system. forgot the actual amount and would have to hunting through receipts, but i'm guessing it was around $500 installed. lol, much better than the thousands i used to spend ;)
anyway, my two cents and it may be an option for you depending on your needs.