Pins are better, but not for all the "wrong" reasons that some people have put forward, such as using them to register against mortises for placement. For most registration purposes, it's absurd to do that as you'd be cutting mortises too close or be cutting too many mortises (dominoes aren't free). The cross stop is an accessory that allows you to do most, if not all, of the registration functions of pins.
The only time that pins excel over paddles is when you want to cut angled mortises on narrow strips, for example, for louver shutters. But it doesn't mean you can't make angled mortises with the paddled DF (see image).
Paddles can be retracted, helpful in some situations, but I don't know if pins can be (someone told me the earlier version of pins could not be retracted. True?).
Here or somewhere else I learned that Festool did not have a patent violation issue with the pins but chose to use paddles. If that was true, the best marketing opportunity (missed?) was to offer an optional pin base for the paddle users. I'd certainly get one as a spare -- for the rare occasions when pins may work better. Or, include both retractable pins and paddles in the base as a new design!
For the majority of DF500 users at any level and furniture makers, I'd argue that the differences between two versions matter little to them in practice.
If I were having two DFs like the OP with one to sell, I'd give the potential buyer a choice: paddles at $x OR pins at $x + a premium.