Just for the record, i am no mechanical, torque/horsepower curve, numbers genious. Just an average rider who's had plenty of seat time on an 01 CBR 929RR and other various 600cc sportbikes and a proud new owner of an S3. I know comparing these two bikes is like comparing apples to oranges and that they are in two different classes, but I thought it would be fun to compare anyway.
I'll start by the gears:
My S3 has about 380 miles on the clock now and i'm starting to test the water in the higher rpm range.
I'm still breaking the bike in, but I decided it was time to see what the S3 had to offer in 1st gear. I ran it up to 10,000rpm and it was fast, but it didn't have that "fly off the back of the seat" pull that the 929 had. Now, I will be honest, I was hoping it would be close to having that hard pull that the 929 has and this isn't a bad thing that it doesn't, because it is still quite fast. Now i'm thinking to my self, "this power has to be somewhere??" So at around 4000 rpm, still in 1st gear, I blipped the throttle, and sure enough the front end came up about six inches with ease. Now this could be done on the 929, but I had to let off the throttle and then twist the throttle quick to get the front end to come up @ 4000 rpm, and it didn't work for me all of the time neither. So now I drop to 2000 rpm on the S3 and hit the throttle hard and the front end comes right up again with ease. I definitely couldn't do this on the 929 at that low of rpm. It could be done with the clutch, but i'm too much of a sally for that. The S3 is a torque monster!
Now in 2nd and 3rd gear, the S3 pulls harder, still not as hard as the 929, but it's enough to get me warm and fuzzy on the inside. However, on the S3, at around 7-8000 rpm, in 2nd gear, you get that "fly off the back of your seat" pull, which was very fun. I wasn't able to see if 3rd or 4th had that same feel in the higher rpm range because I ran out of road

. I would bet, that with a little practice or just a big handful of throttle, that a rider could power wheelie in 2nd gear. I didn't try it because i'm still getting used to the feel of the S3 and i'm also not that great at wheelies.
Here is one of my most favorite things about the S3 compared to the 929: There is roll-on power in just about every gear. I don't have to down shift when I want a power boost like I did on the 929, trying to get the higher rpms for the power. Of course, when you downshifted on the 929, you get the ultimate adrenaline rush of speed. Also, I don't think i'll have to use 6th gear very much on the S3, unless your going really fast.
Suspension and handling-
I don't know much about suspension tuning. My S3 is set to stock and as far as I know, my 929 was also. The 929 was excellent when it came to handling. It was very flickable, due to the fact that I dropped from a 190 rear tire to a 180 rear tire. The 190 seemed like I had to muscle the bike in every turn. The 180 made handling so much easier. The S3 also has a 180 on the back and it seems to me that it is a bit more flickable than the 929 is. Also the shorter wheelbase helps. I haven't been able to get into some good, curvy roads yet, but i'm betting the handling is better than that of the 929. Ride quality is smooth on both bikes.
Ergos-
The S3 is probably a little better in this department, but not by much. My back and wrists are thankful for the S3's straight up riding position, although my wrists got sore towards the end of the day. The 929 also has more of a straight up riding position, which Honda is known for in their sportbike class (at least back then), but not quite as much as the S3. The seat on the 929 isn't the most comfortable and S3 isn't much better, but then again, after riding all day on any sportbike or naked bike, your tail is going to be numb. You get used to it. If you were to compare the ergos of a gixxer or yami to the S3, the S3 would take the cake in my opinion.
Wind protection-
Obviously the S3 has none. I was traveling at about 90 mph with the wind to my back and it wasn't bad at all. You get that "clean air" effect where it just flows around you with no problems. Different story if there is a strong crosswind or if the wind is coming at you from the front at an angle. It felt like I was on a bucking bronco, but then again the wind gust were 40-50 mph. On the 929 it isn't as bad because there is some protection and better aerodynamics. Buffeting or headshake isn't as bad on the S3 as it was on the 929 at higher speeds.
Looks-
My 929 was a very sharp looking bike. I had some nice aftermarket accessories on it and I always kept it in tip-top shape. Very shiny, very clean, never been down. I always recieved compliments on it wherever I went. Then there is the S3. I honestly think it is the sharpest bike i've seen to date. I love the looks of this bike. It has its own unique look that no other bike matches. People look at this bike and have no clue what it is, but they have this look of aw on their faces. Its very funny to watch. Hell, I even catch myself standing in the garage at night staring at it, my wife thinks there is something wrong with me, but it has this ability to pull you in.
Overall, the S3 is the total package--cruiser, sportbike, stuntbike, all in one. There is no way you cannot have fun on this machine. I loved the hell out my 929RR and it has way more top end than the S3, but thats about it. The 929 is a great bike, but the S3 is a better bike in my opinion and i'm looking foward to having it for a long time.
Feel free to post if any of you have had different observations with your S3. I would be interested in knowing what they might be.