Torque curve matters more along with tyres and the length of the swingarm(panigale has bigger swingarm,larger swingarm sends more power to the rear wheel).
Then you have aerodynamics and gear ratios(dukes have the shortest gear ratios of all)
This is the torque curve of a panigale,clearly the torque in the mid and the higher revs is great,great acceleration.
Another thing is ducati has mastered v-twins,they breath better and climb faster and the power band is also very wide delivering amazing acceleration.
The panigale is lighter too.
This is the torque curve of the superduke,the power band is not very wide,the gear ratios help it acheive a good acceleration but they are bogged down by the nature of engine that it is not comfortable at higher revs.
You better ride this bike around 7k-8k rpm.
Ducati 1299 panigale r weighs just 190kgs and the superduke weighs 215 kgs.