This begs the question of whether a person would be leaving the new steed bone stock or not. Knowing this crowd, probably not. So one must factor in the farkle factor to any new bike purchase. As you point out, $1,500 for the pipe and fender treatement.
The little extra umph from a full exhaust is always nice, but on a Busa, you really can feel the weight loss flicking the bike left to right, as all 3 Gen's mufflers are heavy enough to notice when they're gone.
That alone improves the ride.