Hi
When I bought my car (2.5 years ago) the 996 Turbo was seriously under valued and absolute steel, that's why I went for a 996 over a 997 as it was much better value for money. Values have steadily risen since then and the 996 has definitely caught up. So the decision 996/997 is less clear cut. I think it might come down to personal preference.
I went for a car with the X50 power upgrade, not because I wanted the extra power (I'm sure the standard car has more than enough), but I could see it would be more desirable in the future. Apart from that, I think condition, service history and mileage are more important than options etc.
In hindsight I would have bought a manual, I miss that extra level of control. My only misgiving is that the car is so fast and so capable that it's difficult to have real fun on the road without getting into 'lose your licence territory' within a matter of seconds. Frankly the car is far more capable that I am, I'm sure a 997 would be even more like that.
I hope this helps