...I think ours ticks all the boxes!Opinions from people that have different options are always helpful, but looking at this question objectively as someone who has spent the last 10 years selling cars my advice would be to keep it simple.
The Glass's Guide that all dealerships use to value cars breaks each model down into Base +SALT +PEPPER and +CHILI (where applicable) and assumes that all cars have metallic paint and air conditioning. ALL other options are ignored. However, some dealers will take highly desirable options into consideration when valuing a car, but don't count on this. It is also important to note that the resale value of cars fitted with, in the case of Cooper, a PEPPER or CHILI Pack is virtually identical to the difference in the cost new, so either would be equally good value.
From my experience, the Sports Front Seats, Visibility Pack and MFSW are desirable from a dealer's perspective, but things like a Sunroof or White Indicator Lenses are just classed as a bonus.
Also, don't be tempted to go for the cheaper PEPPER Pack but upgrade to 16" alloys and/or part-leather upholstery, as you will lose out long term.
The only other option I would strongly recommend on a Cooper is one of the interior finishes, as the door ellipses otherwise look cheap and nasty. A Colour Line on the other hand will do little or nothing to enhance the value of the car.
Hope this is of at least some help?