Which Boxster S would be a better purchase in the long run?

[tomonomics]

You could also add an extra 8 horses to the 2003S. And remove the roof, radio, and A/C like they did with the Spyder, but you would end up with a car that I would not want to drive very often.

Unless you're building a spec boxster for the track (which I did not think the OP was intending to do), the stock weight/HP numbers are very similar and would not persuade me to buy an older model with more mileage. I guess we'll just agree to disagree.