I'm not sure how much looks will factor into your purchase, but I never cared for the interior of the 996s. I test drove one back to back with the CS and it just seemed "drab" to me.
If depreciation is not a factor, the CS should be your pick hands down. The GT3 may depreciate percentage wise less, but may turn out to be more of a dollar amount. Even with the depreciation, you may be better of with the lower initial "investment" (I use that term VERY loosely) even if it doesn't hold it's value as much.
As great of a car as the GT3 is, the mid-engine platform will always be better, especially if you decide to mod it.
I can assure you, if you go with the CS, you will drive it on the road much more then you plan. It is a pure joy to hop into every morning.
Either way my friend, you are in a great position. Take the next couple months, drive each, and find the exact car you want.
