I have a low level engineer, and I love him, and love pet classes, but without bias or hesitation I have to say that pet pathing is and apparently always will be an issue in any game that has pet classes. I am an MMORPG player of 4 years, and apparently there is something inherently difficult programmatically with creating good pet pathing.
I have bounced around ideas for the solution to this problem for a long time, and the idea I am about to suggest seems to have no exploitable or negative game play consequences that I can think of (although, admittedly, I am no expert).
Simply give pet classes a command (similiar to the pet commands that you can get in the help menu, that will automatically generate a key to be placed as a hotkey) that will summon all pets to the owners side. Make the skill usable only once every 5 seconds, and make it so that the command does not function if the pet is in combat.
I have talked to MANY people and all agree that this would be a wonderful idea (ESPECIALLY in missions) and that if a command like that were made, that the pathing could be left alone and as a player they wouldn't mind. No one would care if their bot ran off in another room if all they had to do was press a button and he would be there at their side.
As I said before, I love pet classes, but from the missions I have been on with engineers, pets in missions are, for the most part, so much of a pain that it makes them almost more trouble then they are worth.
From the little bit of programming knowledge I have, I wouldn't expect this to be a diffult addition to make at all. You already have summoning commands in game that ARKs use, and that engineers use in nano form. Simply take one of those commands, link it to the class in the program that is the pet, put in some commands to check if the pet is engaged in combat, and set it for a 5 second re-use timer.
Just wanted to put the suggestion in front of the masses, and offer a time saving solution for an already overworked team.