There is many examples of what can be done to base system in the above thread .
BMW has an Alpine retrofit kit that is one of the cheapest ways of upgrading the system if you are ultra paranoid about it. It gives you upgraded speakers , tweeters and a decent amp for the front door and under seat speakers.
See the entry in the above thread about Alpine upgrade.
If you want something better many people put aftermarket systems in .
BMW has to prove that it causes a problem before they can deny your
warranty. That being said there is a lot of different treatment between dealers. But it you want seriously better sound see some of the threads on base system upgrade.
Also you might want to identify which system of the three world wide that is in the X3.