Using this logic pets in most other generic MMORPGs are just tools as well because the majority were only useful for:
1. Riding
2. Auto Attacking a.k.a aiding in your DPS.
That is the definition of being a tool. Automata were much more than just "tools" but if you actually played FFXI and actually played PUP, I'm betting you were one of those PUPs who only had the basic 8 attachments and wondered why it did nothing useful.
The storyline itself should tell you they're more than just tools..and hell, the fact it (along with SMNs and their Avatars) has storylines already put it above what the majority of MMOs does with their pet systems. Not to mention, the differences in behavior with the 3 pet jobs was explained pretty well in game:
1. Avatars have a pact with you and depending on that pact affects their behavior, i.e Avatars will auto attack anything that attacks you because their pact is to protect and serve you for proving your worth against them, exception being Carbuncle who joins you of her own free will.
2. Jug Pets are mindless monsters that need guidance to do more than just what their nature intended, thus why them along with Charmed Monsters won't give a shit if your face is being ripped off. The reason enemy Beastmaster's pets attack is due to the fact they have automated mechanics from being NPCs. Something easily changed.
3. Puppetmaster's automata aren't soul less tools, they actually have a soul and they grow with you as long as you program them properly, which is why without proper programming, they won't be as efficient. Their efficiency also lays in how well you as the master know how to use and maintain maneuvers.
This is probably why they're going the cop-out route and using the "essences" system for SMN.
Btw, you're less likely to have a bond with a war lion or war elephant bred only for transport and killing because chances are they weren't bred by you than you are with programmable A.I designed and maintained to your spec, just sayin.

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