The level of complexity in the 996 is higher, so there are more opportunities for issues to arise.
A 993 and a 996 are very different cars, really from different eras.
Cars (like most products) are a trade off between style, design, materials, timing, cost and most importantly for a sports car, weight.
Most of the comments relate to material selection and design. The interior is not as solid as some other cars, the indicator stalks do initially feel cheap and flimsy, but they do the job and don't weigh much.
On the earlier 996's the plastics were not that great.
But this is not what the car is about - it is not about luxury. It has enough to remain broadly competitive, but it is not its strongest point.
Mechanically, the engine is more sophisticated, with variable valve timing and variable lift, electronic throttle, traction control, stability control, etc. The gearbox for the 996 was redesigned to handle more power yet weighs less than on the 993. I posted on the 993 forum a while ago a detailed comparison between 996 and 993.
The shell of the 996 is much stiffer than the 993, so give a better platform against which to work.
The car is more modern all over, so it is not really a fair comparison.
The 993 is a fine car with a distinct character, and I would love a 993 GT2, but I can't have everything.
All cars have issues, whatever you pay for it. The JD power survey shows (together with anecdotal evidence) that many prestige brands do less well than more mundane brands. However, Porsche consistently does well.
Although some people have had issues, many people have not.
The most common thing seems to be oil leaks, although not all cars are affected.
Engines have failed, but compared to the 10s of thousands of 996's sold, not that high a proportion.
The issue is that if something big does fail, it costs a lot of money.
This is where the warranty is to be recommended. You can renew every year, up to 9 or 10 years old and 100K miles (although someone posted recently this is now 125K, but I am not sure if this is just for the 997).
I genuinely believe that you will almost certainly be OK, and no worse off that with any other car.
Regular use is the best thing for it.
Certain precautions are wise to ensure optimal use, such as allowing the car to warm up before using max throttle and revs, making sure the oil level is OK at all times, drying the brakes after washing the car, not braking hard then sitting with your foot on the brake (baking the pads onto the discs - use the handbrake), trying to be smooth with your inputs and not missing gears.