The 996 is the total package, it has no drawbacks to speak of.
The 993s got hot. Very hot. They had a huge oil sump taking over 10qts of oil to aid in cooling the engine and the turbo, under sustained abuse, they would start to see heat related issues. Porsche was ready for something new, you're right, their engines needed to be modernized, and when they did it, they found it better to water cool. They could have made all of the advancements they did and keep it air, but they could push harder on the engine with more reliable performance with water. Water cooling a rear engine car isn't fun either, they needed good reason to do it.
I'll say any of the 911 996 6spd Twin Turbos. They are just the total package. There are extremely few SUPERCARS at any price that can top 911 in all areas.
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