A watercooled 911 is VERY different from an aircooled 911, in just about everyway possible.
If you've never experienced an aircooler, thats fine. In many ways (effective HVAC, Powersteering) a 996 will be like a nicely upgraded 944. Modern, comfortable and way faster though
As mentioned, IMS is a big issue. Other issues of early motors were "d chunking" of cylinders, Coolant tank failures, ignition switches too. No "worse" than what a typical 944 owner would be used to.
Some also say that buying a "low miles" example will be more troublesome. Something about when the cars are used everyday, they seem to have lower rates of failure. Internet conjecture to be sure, but I think an item used everyday would have fewer issues than one used 1-4 times/month for instance.
Most "early" cars have already failed by this time. That said, should you need a replacement 3.4, I am told they are getting a bit more expensive. I'd figure maybe $4-8K used, installed up to maybe $15K for a new one. Hmm.. another similarity to a 944.. sometimes replacing a broken component is equal to the value of the actual car. D'oh!
Go for it!