1) Scarcity - 993's and 964's were made in much smaller numbers than the 996
2) "Air cooled". These words define the 911 perhaps more than any other element. Many feel that once the 911 was no longer aircooled, it was no longer a "911" in the true sense
3) Reliability. There were some reliability issues with the early 996's. It wasn't until CEL and Valvue guide problems for the 993's reared their head that they were "more reliable"
I too love the early cars vs the later cars. People complain about the increased weight of the newer cars (hmm, while quick to point out the A/C, pwer seats etc, they almost NEVER complain about the increased weight of the 3.6 liter 280hp motor, or the big heavy exhaust, or the large 18" wheels that make it handle well, but I digress

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To me, the 996 is the new "middle year" car. Much maligned like the 1974-77 cars. BUT. A 996 is faster than a 993. Should be enough to compel anyone to get one, especially if they are "cheaper".
Believe it or not, there are some Porsche fans who think the 911 was a sell out compared to their 4-cyl 356.. Others hate the 924/44/68 series cars, other the 928. Every time Porsche builds "a better Porsche" people rise up as though Porsche has insulted them by improoving the breed