An aftermarket exhaust may or may not increase the performance of the car, probably guaranteed to make it louder though.
MINI should sell this kit with a guarantee on the power increase. It will also be fully protected by a warranty and easier to sell on or trade in against another MINI.
The JCW tuning kit cars carry hardly any premium over a stock Cooper S come release time. I know this as a few years back I bought a second hand R56 Cooper S with the JCW tuning kit. It cost very little extra over and above other stock Cooper S models on the market at the time!
The MINI supplied JCW tuning kit will only be making its power through the ECU remap associated with the kit. The exhaust, much like the other aftermarket options available, will make little to no power increase. To get power increases from the exhaust system you need to look at the downpipe side of things.
So you are paying a £1k premium over and above the cost an aftermarket exhaust like the Remus (which is of equal quality to the JCW system, and louder) for a very minor ECU tune and 2 x JCW badges for the front and rear - which is rather steep!
I have no doubt it will sell like hot cakes though as the warranty protection is the main selling point for a kit like this!
