Had the exact same dilemma before I bought my R56 Cooper S as I looked at a few GP's.
There's no doubting the GP is an absoltuely brilliant car and offers a lot in terms of a rewarding drive but I opted for the R56 as it offers the more complete package. Added to the fact i'm a bit of a gadget geek and you have to bear in mind the GP's have nothing in terms of spec. Even xenons are forfeited which put me off greatly.
I would say, however that the GP is a more striking car to look at than a standard R56, but in terms of an all round package - the R56 takes it every time. It's an absolute hoot and I don't regret my decision at all.