The only "cool features" the Pre has is a more open system, based on Linux. You can AFAIK distribute your apps without going through their approval process, right?
The 3GS solves most of my gripes with the iPhone platform: video, decent RAM, decent storage (32Gb), HSDPA.
my choice, iPhone. buying a Pre now is buying a version 1 of a product. It looks nice on paper but you never know. The iPhone has a nice set of apps and the new 3GS has awesome hardware. I'm buying a 3GS as soon as possible :)