Honestly, I have the upgraded sound system in my box and it sounds just fine. I got it that way when I bought it so it was money saved by the time the final deal was worked out.
I do plan on replacing the Bazooka tube but only because I want that space regained. I'm weighing my options and I like the under seat idea for the bass speakers. One bass speaker will do me just fine. I like to feel my music but I don't want to advertise.
What I'd really like to do is change the actual head unit to something more iPod friendly.
So I guess I'm the only one here that gives the stock upgraded sound system a thumbs up. Now to totally contradict myself in a way. If you do not have this option yet and are thinking about getting it in a new xB... DON'T! Save your money and space in the back. Get an after market!

You will most likely be happier with the extra money and space saved.