I just prefer the stock stereo look. The audio system of our Jetta isn't modified, and won't be.
We park it on the street (no garage space), so putting an aftermarket stereo in it could make it more enticing for break-ins.
I can understand your frustration with multiple sources and the stock HU limitations. If I were trying to do the same, I'd probably be looking at an aftermarket HU as well. (At least the Jetta is a standard size unit, as opposed to the oversized/oddball Symphony stereo in my Audi A4! :-P)
The only other question I have back at you is why in the heck would you need all three sources? The PB easily replaces the CD changer, hands down. I can *almost* understand wanting SAT radio if you're into it, but a 20gb (or bigger if hacked) PB seems like it'd be plenty...
Subwoofer control isn't hard to have installed, and if it's properly crossed over and tapped to a line level converter, I'd guess you'd be hard pressed to notice a difference in sound quality.
Then again, if you're a hardcore audiophile, ignore my comments; replacing the stock system is about the only option at that point.
-Cheers,
Steveo