That depends....how long have you had your M3? I say go for the M6. But the Supercharger systems make the car whole different animal. but then youll want to spend money on new brakes and etc.
When it comes to mods** to the engine and brakes i prefer them from the manufacturer.
'16 /// M3
'15 /// M4 -Sold
'11 E92 ///M3 ZCP - Space Gray - Sold
'11 E92 ///M3 ZCP AW- Sold
'06 E46 ///M3 ZCP JB- Sold