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IMHO, the 2005 & 2006 models have a better tranny than earlier models. After 2006, (the end of 1st generation), the engines and body panels are different on the 2nd generation model years. In the S model, the 1st gens are super-charged and the 2nd gens are turbo-charged; again, a different design, but both gens are pretty solid from 2005 on.
IMHO, the 2005 & 2006 models have a better tranny than earlier models.
Different ratios, but not necessarily better. The spacing is wider across the first 3 gears in the later version, and all gears have lower ratios. Basically, the later transmission took 1st and 2nd way down and 3rd+ down a bit. This gives it more "usable" gearing in stop and go city traffic, but not so for high-speed/high-rev work, especially given the wider spacing between 2nd and 3rd. If you are running even a bit more than stock torque and hp, then the earlier transmission is actually a better choice as it offers closer ratios and still gives you enough off the line grunt. (If you need off the line grunt. Which personally I do not.) For the standard ~200whp modified car, I would argue the earlier transmission is the one you want.
2003 MCS with 63,000 miles and no major issues. When I was looking I knew I did not want a 2002. Some say even 2003 models have problems that still need working out but I guess my very late production 2003 had those addressed. I personally would steer clear of any 2002-2006 standard cooper just because of the midlands transmission. I also would not want a CVT because I have read about a lot of problems with those. However any online forum will only have the people with problems posting. If a car works then the owner won't post anything because its suppose to work and thats what is expected.