I bought my 986S Boxster right before the 987 was unveiled.
I could have bought newer (mine is 2000) but the mileage was so low that I couldn't go along with the 'buy the newest you can afford". Actually I spent WAY less than I could have. I saw no point.
A massive chunk of the depreciation had been absorbed by the previous owner and the car was basically show room new. It was an S in the silver and red I had to have. All bases covered and I sent the bank half the loan check back to them.
The 550 was still in the showroom when I first saw it. This car looks the way all the Boxsters should have come out of the factory. The chrome trim and cocoa leather made it look like a much more expensive car. The only thing I didn't like was that it was missing red brakes.
I'd get the 550 and swap to a CPO'd 3.4 987S in a few years when they are closer to the depreciation 'plateau'. You might have a real hard time parting with that 550 though...