I changed my 987.1 Boxster S for an S5 cabrio. Both are great cars with good performance and handling. The S5 offers (a lot) more comfort than the Boxster. On the other hand, few cars can enter a corner as precise and quick as the Boxster.
With the top up the S5 feels more like a coupe with a metal roof, while the Boxster still feels like a cabrio. With the top up the windnoise at higher speeds (+200km/h) is a lot louder in the Boxster. With the top down there is less wind in S5. Last weekend we were in Germany and did 220km/h with the top down. Could hardly notice any wind or noise. With the Boxster that would look like you spent a night sleeping in a wind tunnel
For more spirited driving the Boxster certainly wins. While the straightline performance feel equal, the cornering capabilities and balance of the Boxster is superior. In this sense the S5 feels more like an oil tanker. Serious amount of understeer (as with most Audi quattro cars).
If you don't need the rear seats and don't intend to use the car every day all-year-round then I would take the Boxster. Otherwise the S5.
I am very happy with the change and don't miss the Boxster (but I have a 911 to make up for the loss). The supercharged V6 in the S5 is a sweet engine. Plenty of low-end torque and revving freely to the redline. The S-tronic gearbox in the S5 is the same design as the PDK (it was specifically designed by Audi for the S5). It is very, very quick and suits the engine well. Downshifts with the paddles will cause a stupid grin on your face Four adults sit well without feeling cramped. The ability to fold the rear seats makes it very functional if you need to transport stuff, e.g. skis or snowboards.
So, it all comes down to what you want
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Porsche 997 Carrera S in Carrara White with black leather interior. PASM-Sport Suspension (-20 mm), PSE.
Audi S5 cabrio in Ibis White with black leather interior.