To try and answer your questions:
1. Grey with black trim is available in all years of MINI production.
2. There have been many changes since the Cooper S was first introduced. To summarise pages of information into about 3 lines (if that's possible!)
2002-2004: Pre facelift 163 bhp supercharged Cooper S
2004-2006: Post facelift 170 bhp supercharged Cooper S
2006-now: Second generation 175 turbocharged Cooper S
There was nothing wrong with the 2002-2004 car, though the 2004-2006 car offers a lot of small improvements, if the funds can run to it. They are both highly tunable and robust, though the fuel economy can suffer if you use the performance

The supercharger is amazing, not only does it make a great noise, but the reaction is instant with none of the lag associated with turbos (though the fuel economy suffers!) The high point of Cooper S production so far, in my opinion.
2006 onwards car is a matter of taste. It's definitely more economical (by about 10-15%), more comfortable, quieter, safer and easier to drive, though the looks and driver feedback are the subject of much
controversial debate and cost cutting is apparent. See and try one for yourself, then decide.
Look out for the "Works" version of any generation which will have 200 (02-04), 210 (04-06) or 211bhp (08 onwards).
Whatever you do, go and buy one; you'll love it and save a pile of cash in comparison to driving the LR!
Tigger.