Manuevers allow a PUP to use their pet's abilities which is the main aspect of their job, they're not Monks so DDing on the master isn't 100% of their job, half of their job is the Automaton which is how SE justifies the delay.
Difficulty:

To enhance your automaton's performance, you have to sacrifice your own (both in JA delay from maneuvers and in equipment). To boost your own performance, you have to sacrifice the automaton's, and furthermore alter its behavior in an undesirable way. The benefits of enhancing one or the other basically cancel eachother out. Cutting down JA delay, making the time investment in boosting your auto smaller makes boosting your automaton more worthwhile.