Most likely because they were the first combiner. So, having the robot who forms the torso/head always being the leader (ad nauseum) of the various merging groups hadn't become the norm yet. Scrapper was always the more interesting character (in my opinion) anyway.
All those moments will be lost in time, like tears in rain. Time to die.
Still it is my suspicion that there was a miss-communication between marketing and the animators. Hook should be the leader as he forms the head.
The only reason Scrapper had the best lines is because he was designated the leader. If Hook had been cast as the leader, then he would have gotten all of Scrapper's lines.
I like Hook's voice. He sounded more refined and more experienced.
Some people have said that Hook was the smartest Constructicon so he formed the head. However, being the smartest doesn't make you the leader. Guys like Perceptor and Wheeljack are smarter than Optimus, but they aren't the Autobot leader.
In the Dream wave character bio books, his profile says that Megatron chose Scrapper as leader over the "snobbish" Hook. Probably for being more humble and following orders to the letter where Hook came off as an elitist douche that could rub cons the wrong way.
I read up on the profiles in Transformers wiki. Hook is only second in command to Scrapper, the logic behind it seems to be like how Megatron mentioned Shockwave being humble and respectful. Scrapper is just that. Hook is pretty much as bad as Blast Off when it comes to snobish behavior.