I must add to all of this since I've logged over 50k miles on non "big" bikes over the last five years. Previous bikes were 2000 CBR F4, RC51, 01 GSX-R750, & 05 GSX-R1000.
I must say there are definitely a few things that you guys are missing here. First of all, the new supersport bikes have gotten smaller, and for me less comfortable, especially the seats. The 01-02 GSX-R1000 was a super comfy bike for me (6'1" and 215 at the time). My last bike, the 05 1K, I had dropped weight down to 200lbs and it was still uncomfotable because of the narrow seat and aggressive riding position. I rode a friends 01 750 this fall and I'm now 175lbs and it was nice.
Now, what many are forgetting. You can easy change the handling of these bike without spending much money at all if you feel they are twitchy. First; tires come into play big time. two; drop the rear slightly even if it's just 1/2in. This will help!!! Then you can look into bar risers, different grips, different seats and such to help out a bit on the comfort level. You'll never have the ride quality of a busa, I don't think it's possible because the lack of weight on the 1k's just doesn't absorb the road like a busa.
Now for the power. I don't quite understand why people say the 1k's don't have low end power. My 05 GSX-R1000 was a monster with a full pipe and tuned. You simply don't ride these bikes at 4,000rpms or less. The motors were not designed to do that. Once you hit about 3,500rpm (on the GSX-R) the motor starts to smooth out and by 4k it's golden and making power! I believe somewhere in the 65ft lbs at 4,000rpm...which compared to the weight and with proper gearing will be enough to satisfy your normal rider. Heck the front tire starts to pull off the ground at 6k on many of the bikes so what more can you ask for.
I used to ride a big bore ZX12R (I know, I was a trader) and all my friends had liter bikes. My 12 was making 190rwhp and 110ft lbs so it was no slouch. My buddies that had properly setup 1k's (pipes, PC's, geared, but nothing major) could keep up with me pretty much everywhere except if we pulled away from 60mph in 5th or 6th gear, but that was because they were turning such low rpm's that it wasn't even fair.
anyways. I think to truly understand the difference you need to log over 1,000 miles and make some changes to a liter bike before you can make an argument about if they are the bike for you.
ok, enough rambling!