I bought a base (2.0l) Cayman off the dealer's lot and considered this question after the fact wondering if I'd done the right thing. My conclusion was that I had made the right choice. Here are some of my thoughts, some less important than others, some possibly just rationalizations:
The S model is marginally heavier though probably not enough to notice. Some of that will be from other hardware, I suspect. The S has other features that I really don't need, would rather not have. On the other hand, my car has the 20" wheels...
At the EPA mileage estimates (which I have found to be reasonably accurate in my usage), the difference in price is enough to pay for all the gas you will use through at least half and maybe even all the life of the car. The gas savings from the higher gas mileage contributes even more.
At the EPA mileage estimates, the 16gal tank on the S has a similar single-tank range as the 14gal tank on the base model.
In theory, in the smaller engine there should be lighter loads on the main, con rod, and wrist pin bearings, and therefore possibly longer life. Of course if Porsche engineers compensated by using smaller bearings, this point doesn't hold. You'd have to ask a mechanic about this, and I suspect the engines haven't been out long enough for any real data to exist.
In theory the smaller engine might be able to rev more easily. Of course that's just a traditional argument that may not apply at all in practice.
You (or at least I) would have a hard time telling the difference between the two engines in normal use. Personally I have almost no opportunity to exercise mine to its fullest "potential" and when I do it wouldn't matter doodleysquat whether I had the extra oomph or not. It gets going real fast real fast.
Other folks will have different opinions, of course. If I had bought the S model I would not be able to justify it. Some would say I can't justify having bought a 718 Cayman at all, but that's a different discussion!
Jim, on my second Porsche. The first was a 912 in a long time ago in a galaxy far, far away.