Did not realize you don't have a MINI yet - definitely if you are considering aftermarket stereo, DON'T start with the HK! The HK is for people who are satisfied with what it offers.
I ordered it unseen, and was not satisfied - that eventually forced my development of the HKenabler circuit, but it is a compromise solution.
Of course, a good aftermarket system will cost you more than the HK package.
The front doors *can* take a 6.5" speaker with appropriate adaptors; the rears are 6x9 unless you are planning a convertible (which I think has the 6.5" again).
Here is a fabulous strip down / upgrade sequence put together by Paul - it will give you some idea of the work involved!