I've only heard one Bose system in a friends car and I've got to be honest, I thought it sounded pants. Upgraded my own speakers and head unit to aftermarket a little while back and think it sounds much better than the Bose I heard and was a relatively easy job to do.
As far as other things you can do to it, it depends how deep your pockets are really. Their is so much that can be done. If you search on here for "a3 mods" their are a couple of threads where people have compiled a list of some of the cheaper and easier mods, may be worth looking at these first to get you started.
Hope this helps anyway, and most of all enjoy the car and enjoy the forum. Plenty of ideas on here and plenty of helpful people if you're ever in a spot of bother and need an answer quick.