Of course the 996 is a better car in terms of performance, comfort, safety etc. Having said that, 993 is definitely more desirable for being the last air-cooled 911, classic design etc.
I think the 996 is coming back into fashion though, especially the earlier more analog models that didn't have a lot of electronic nannies. Also, you can buy one for a lot less than a 964 or 993 and not have to worry about driving it. 964 and 993 prices are insane. The 964 was once the orphan child of the air-cooled 911 lineup. Times have sure changed.