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I guess it all depends on mileage. They are both weekend/track cars for me, so I don't drive them much. I do about one track day a month. Like the E46, the 997 GT3s require some preventative maintenance, such as pinning coolant lines and differential upgrade. I track mine, so I changed out some other things. It is a bit more expensive to maintain than an E46, but I think it's still pretty reasonable. For comparison, a Nissan GTR has some outrageous maintenance costs.
Based on your profile name, I'll assume you came from or currently have an e46 M3 and a 997.2 GT3. I'm in the process of selling my e46 M3 and looking to get a 997.1 GT3. From your experience, what sort of maintenance am I looking at from a cost perspective. My M3 has been relatively maintenance (issues) free - very pleasant experience. I've heard GT3 owners come from both sides of the aisle - "just like a regular car, change fluids and spark plugs based on time/mileage," but also "thousands of dollars each year in maintenance."