I put forth this idea (buried in my megapost), that would allow Puppetmasters a great deal more control over their automaton's decisions.

The concept is Automaton AI cards.
Soul Plates can be turned into Artificial Intelligence program cards for Automatons. These are equipped like attachments in 2 new slots (not attachment slots) one in the head, one in the body, and they change the AI of the Automaton, giving players control over the abilities used by the automaton and access to new abilities and traits.

These AI Cards are separated into two groups: Weapon and Ether Control Cards. While they only drop from Archaic Machinery (Gears, Chariots, Ramparts), many Soul Plate cards can be used in the creation of AI cards to enable other special properties. Ether Control Cards can only be created from soul plates taken of enemies with mage jobs. (AI cards are added to the Automaton's attachment list, or something exactly like it, only for cards.)

I'll copy-paste/hide the post here for further discussion in this thread, rather than the megapost.

Details about Automaton AI Control Cards
Based on Empress Jubleel's research into programming Automatons so they could act on their own without direct control of every action by their Puppeteer, the Simulacrum scientists have created new programming AI cards to modify the actions of Automatons using the traits and tendencies of creatures whose data has been recorded on soul plates.

I'd only expect an On/Off sort of system, or choosing triggers from the elemental list, but if a rudimentary "Gambit" system could be put in place for more precise control, it would be even better, though not a realistic expectation. For those who think Pup already has enough control of their automaton through maneuvers, I think it's far too limiting, and new attachments keep eating active maneuvers, ruining control setups, both for weaponskills and magic priorities.)

AI cards can be switched out on the fly, and flipping abilities and spells on and off can be done without deactivating the automaton, unlike attachments. (Switching any option on or off will reset all hidden ability timers for abilities like Shock Absorber, ranged attack and spellcasting cooldown as if they had just been used.)

All Weapon Control Cards (WCC): (placed in the body slot)
* Enable/Disable weaponskills and abilities from a menu.
* Last used Control checklist should be saved for each Head/Frame combination. (I won't suggest this for each AI card)
* This removes maneuvers from the weaponskill priority system.

Weapon Control Cards created from most enemies simply grant the generic job traits of the source monster's job to the Automaton. Bosses sometimes grant unique traits and the occasional abilities to the automaton.

Sapling WCC: Adds Warrior job traits to the automaton. (perhaps add Beast Killer and weakness to Plantoid killer)
Archaic Gear WCC: Adds Warrior job traits and adds Restoral to the weaponskill list.
Archaic Rampart WCC: Adds Beastmaster job traits to the automaton.
LBC WCC: (Long-Bowed Chariot) Adds a version of Homing Missile to the weaponskill list.
Gurfurlur WCC: Adds versions of Haymaker and Sledgehammer to the weaponskill list.
Cerberus WCC: Adds a potent triple attack trait. Greatly reduces Fire maneuver overload rate.

Menu: (Valoredge head/body with Archaic Gear WCC)
Abilities Control
Shield Bash . . . Use
Chimera Ripper. . off
String Clipper. . off
Cannibal Blade. . Use (Maneuver priority may be set here instead of just turning it on, selecting the element you want to use to trigger this weaponskill)
Bone Crusher. . . off
String Shredder . Use
Restoral. . . . . Use

All Ether Control Cards (ECC): (placed in the head slot)
* Enable/Disable spells from a menu.
* Ether Control Cards often add all the spells of their source monster's job.
* Cards can also add an AI tendency to prefer certain spells over others.
* Maneuvers now only control attachments, not AI.
* Last used Control checklist should be saved for each Head/Frame combination. (I won't suggest this for each AI card)
* The menu for spells cannot be as detailed as Weaponskills since there are so many more options. They should be grouped together, such as:

Spells . . . . . . . . Control
"Enfeebles". . . . . . . off
Elemental Magic Tier I . off
Elemental Magic Tier II. off
Elemental Magic Tier III off
Elemental Magic Tier IV. Use
Elemental Magic Tier V . Use
Status Removal(self) . . off
Status Removal(master) . off
Cure (self). . . . . . . off
Cure (master). . . . . . Use
Cure I . . . . . . . . . off
Cure II. . . . . . . . . off
Cure III . . . . . . . . Use
Cure IV. . . . . . . . . Use
Cure V . . . . . . . . . Use
Cure VI. . . . . . . . . off
Drain (under 50% HP) . . Use (possibly options for Drain, like "Under 25%/Under 50%/Under 75%HP)
Aspir (under 25% MP) . . Use (possibly options for Aspir, like "Under 25%/Under 50%/Under 75%MP)
Haste(self). . . . . . . Use
Haste(master). . . . . . Use

The list would auto-trim down to only those spells available with the Head/Frame combination in use.

Example Ether Control Cards:
Hilltroll PLD ECC: Adds all Paladin spells to the magic list. Prioritizes Flash, Self-Cures.
Wind Elemental ECC: Adds Tornado, Blink and Haste to the magic list. Prioritizes Blink on Soulsoother/Harlequin, Tornado on Spiritreaver/Stormwaker.

From my perspective, most of the issues I have with the automaton AI would be fixed with something like this. Maneuvers would be used to manage attachments, not convoluted AI. It also opens up a whole new world of AI cards that give new special attacks, spells, job traits and innate status effects.