The BOSE system is definitely better than the standard system. It is also nicely integrated, and the sub doesn't take up much space in the back. Interestingly, the sub in the SW is much smaller than the saloon/sedan (something like 5.25" vs 10").
Now, compared with a quality aftermarket system, BOSE does not sound that great. But an aftermarket system may not integrate as nicely, requires work done on the car (ie: door trims removed, dash trims removed, door sills for wiring, etc). For aftermarket to sound great, you have to spend 'great' too. If you spend similar money to BOSE on an aftermarket system, you'd only expect a subwoofer sitting in a subbox plonked in the middle of the boot; highly professional installation (ie: no damage to trims, no new rattles, properly mounted speakers, neat cabling all cable-tied, etc) and a part-fibreglass subbox integrated into the side of the boot, will skyrocket your costs.
Hence, BOSE is a good middle-ground to most people who I'd call 'non-enthusiasts'. If you are a genuine ICE enthusiast, you'd go aftermarket. If you don't really care much for music quality, you'd probably be happy with the standard setup.
Having said this, I'm an ICE nutter. But our SW is primarily the family car driven by my wife. So the BOSE system suffices cos I don't wish to mess with this car or lose boot space. I'm sure my wife would be happy with the standard setup; and I'm satisfied with the BOSE. Mind you, BOSE was standard in our Ti Oz-spec car.