As KPKalle has said, which one do you prefer driving?
One being a preferable colour or having less miles on the clock is one thing... but the Cooper (especially the auto) and the MCS
are totally different cars. I would go for the S personally but I know people who just plain dislike the S and much prefer the standard Cooper. I happen to prefer the extra grunt and speed of the S, along with the supercharger whine (and to be honest, the auto gearbox doesn't really lend itself to the MINI in any form - it's too much of a drivers car not to be a manual).
Drive them both back-to-back, then make a decision.