Two completely different cars. I would drive the S before buying. There are performance gains in the S over the standard, but can you use them on the street? The resale is better, but you're already in a Boxster and are losing value. If youtrade, you will lose even more money for a small gain in HP and brakes.
I'll admit that while in a pack of healthy newer and older 911s, my Box won't accerlate as fast, but, with the exception of 993s>, I can keep up in the corners. Performance cars today are not made to use 100% unless you are on the track. They are too good for the roads we use. We don't have an Autobahn.
Boxsters don't make good track cars because they require full roll cages to run in most places/groups.
I'd enjoy the car the way it is. Just my $.02.