In April 2001, I bought a 2001 Carbon Black BMW E46 M3 6-spd and I was very excited about it at that time. I had a 1997 E36 M3 before and figured out that I can use the more advance technology that BMW put in their engine, producing an extra 93 hp from the previous generation M3. 
I was really excited with my new car in the first few months but then I felt something is missing from it. I felt that I like the handling of my previous E36 M3 better, I also felt that the steering feel of the new car is a bit light, giving me a less road feel/feedback than the older M3 and personally I felt that the new M3 is a bit too big for a sports car. Oh and I personally don’t like the raspy sound of the exhaust when I rev’ed up the engine either. 
But other than that, the new M3 is obviously faster and comfortable (roomier, very comfortable sport seats, NAV, and other comfort features). 
A friend of mine who is an excellent driver on and off the track, complained about warping the rotors and running out of brake pads of his E46 M3 everytime he comes home from a driving event. So he tried to fix this problem by replacing the rotors with the Euro Cross-drilled rotors but it did not help him. He finally found what he was looking for with the Brembo Big Brakes Kit and so far he is very happy with it. So if you are into driving the M3 on the track, it is highly recommended that you upgrade the brakes on this car. 
A few months after owning the M3, I felt dissatisfied with the reasons I mentioned above. I felt that I should have kept my previous M3. Well I always wanted a Porsche, specifically the 993 model so I started to send emails to some 993 owners that I met from Rennlist or from Tracquest driving events. In my emails, I was asking for advices and inputs from these 993 owners and they really helped me a lot. I really appreciate their help during my search 
It took me approximately 2 months to find the 993 that I’ve been looking for. During my search, I considered cars from other states as well (Florida, Virginia, Georgia, etc.) but I decided that with this kind of money I will not buy a car that I have never seen before and of course I would like to have the car PPI’ed before I made a decision to buy it. Eventually I am very grateful that I was able to find a mint Silver on Black 993 C4S at a local dealer here in the SF Bay area. I bought my 1997 993 C4S on Oct 31st, 2001. This car is literally a dream come true to me, I have never thought that I will own a Porsche before and I am very very happy with this car to say the least. 
From my short experience with the 993 and my amateur/beginner’s driving skills on the track, here are my comparisons between the 993 and the E46 M3. 

Acceleration: Obviously, the M3 is faster than the 993. From the seat of the pants, I can also feel that the M3 has more torque than the 993. The acceleration response of this car when you step on the gas pedal is just amazing. In my opinion, the new M3 has the best natural aspirated inline-six engine so far. 

Handling: I like the handling of the 993 much much better than the M3. Even though I think the M3 is more forgiving (especially with its DSC on) but I feel more connected with the feedback in my 993. The 993 also feels more planted than the M3 and I am hoping to make my 993 a better handling car with the PSS-9 kit that I am ordering now. Oh… that and of course, learning on how to drive the car on the track. 

Interior: Obviously you can fit more people (or dogs?) in the M3 and you have more comfort-feature too in the M3. I overheard somebody saying that the dashboard of the 993 looks like that in the U-haul truck. Well, I personally like the dashboard of the 993 because all that I need is there and I do not need and do not like the luxurious (or yuppy?) Jaguar/Benz/Lexus dashboard design. 

Styling: How could you compare the classic line of a 993 with the styling of the M3? In my opinion the 993 looks much much better than the M3. A while ago when I was still dreaming about the 993 (I still am), I was walking with my fiancée in downtown Los Gatos and saw a parked Silver 993 C4S. My fiancée was going into a store and I told her if I could wait outside instead of going into the store with her. She said yes, so I was standing outside and staring at the 993 until she got out of the store. I still do that every now and then when I go downstairs to my garage to take a peek at the 993. 

Brakes: The Big Red wins… hands down 

Driving Experience: Every week, I am always looking forward to Saturday morning when I can drive my 993 on an empty backroads/mountain roads here and … take a picture of some cows (just kidding Matt). It is a stress relieve for me and I really enjoy it. All I can say is that so far my experience with the 993 has been really great and I am hoping that I will not have to sell my 993 ever. I am thankful to God that I am given the privilege to own and drive this amazing car. 

Thank you for reading….. oh and of course, this is just my personal opinion/review. Others may vary.
 

Martono, Suwipin (pin)