Warranty is always nice to have, especially given that the MINI is an expensive car to fix when something goes wrong. HOWEVER, it'll only be a limited/extended warranty, so if I'm not mistaken, it'll not cover everything that a warranty from new would have covered.
If you're confident that the cheaper car is in good shape and has been well cared for, the Cherished warranty probably isn't worth £2k extra.
Aside from the skirts, I'm not a massive fan of the whole first gen Aero kit (as MINIAC said, there's no JCW kit, but the Aero kit was often fitted to the JCW). The skirts really finish the car off and are worth having... the rest of the kit always looked a bit cheap to me.
Bigger brakes are a massive benefit on the JCW, but it's more cost effective to go down the aftermarket route IMO.
The Recaro seats were a fortune to spec, plus they're a huge improvement over the standard sports seats. Also, fitting some form of tidy iPod connection will cost very little, so don't get hung up about that.
I guess that's my 3p now.