At any RPM the 1199 has far more torque than the 998. Look at some dyno graphs. Of course, to be completely accurate you'd have to dyno 'em both back to back on the same dyno, but there's as much as a 20 ft/lb difference under 5k rpm. And even if the torque comparison was roughly the same, the extra 60 horsepower are hard to ignore.
The 1199 destroys the 998 everywhere, everytime, in every category. 998s are great bikes, but absolutely nothing compared to the Panigale.