Very simple.

Make it so when you use "Obey", it toggles the pet behavior.
Currently Obey is a command that tells your pet to attack, why not just make it a stance of some sort?

Sic then becomes a generic attack command, and your pet will either use the special skills if Obey is off, or refrain from using them if Obey is on.

This would bring a LOT of control to the Arcanist class, and prevent a lot of accidental skill use. Emerald Carbuncle/Garuda using their level 40 skill with no DoTs on the mob because you didn't tell it to Obey is awful.

Another great feature would be to automatically make your pet "Heel" when you run too far after using "Place". Often times I see people do this, then they run out of range of their pet and it unsummons.