Mercedes out of the factory in the USA come with fairly good stereos. They can be upgraded but there are two different philosophies:
Theory of Constraints
Find the issues that hold back the factory system and address them.
Replace Front Woofers
In this method which, isn't a bad way to start. The best things to address are the "front woofers" which Mercedes uses bigger 6.5-8" woofers in the front doors or footwell etc to provide strong mid-bass. I would 100% recommend just upgrading the front woofers as a good way to start. WoofersEtc sells Dynaudio woofers ala carte and you may just want to drop those in.
Add some dynamat and the factory system is instantly improved with just adding front woofers.
Unhook the factory subwoofer, do a bit of research on the wiring as you can likely tap it. Add in subwoofers. In this case 2x 8" or 2x 10" woofers are ideal to complement the factory setup.
Sum, Process, and Replace
Sum the signal, Process it, Put it out to a completely aftermarket system.
I say completely because at this point that is what you should do. If you sum and leave a factory mid-woofer it isn't ideal. At this point you'd likely aim for high quality 4 speaker setup with subwoofers. Take out every driver, replace them, in this method the way to really get the best results is to ensure everything is aftermarket matched. Don't even leave a capacitor.
Which ever way you proceed, or even if you don't upgrade your audio system you may want to consider adding Dynamat. Dynamat uses aluminum combined with butyl rubber to absorb and dampen resonate frequencies. This can make a big impact and will be the source of an upcoming series.