I think what needs to happen is being able to summon both Eos/Selene and Emerald/Topaz Carbuncle at the same time (But you can't summon your companion then) in the overworld area. There are logical reasons why this is impossible (the pet-based skills eg Rouse could only target one pet) like too many pet bars to micromanage. Whatever gets/needed to be added has to be a self-contained AI more like the Chocobo and AI NPC's where you pre-program it to think for itself instead of being micromanaged.

But at that point, we're playing a different game. Mabinogi had a very versatile pet AI programming that was marred by hackers making the pets do stupid and impolite things, so a lot of the power of it got nerfed (making "chase AI"'s and "pokemon AI"'s were some overly-ambitious AI's) .

What perhaps would suit FFXIV is to have a more simple "Pet Macro" that just creates a decision tree based on what the scholar/summoner selects without the overly ambitious lists of monsters and behaviors to respond to. eg...
To use (skill) when ready
.If not in Party then:
..(skill) Me when HP <80%

.If in Party:
..(skill) Me when HP <80% OR
..(skill) First Tank when HP <80% OR
..(skill) Second Tank when HP <80% OR
..(skill) Second Healer when HP <80% OR
..(skill) First DPS when HP <80% OR
..(skill) Second DPS when HP <80% OR
..(skill) Third DPS when HP <80% OR
..(skill) Fourth DPS when HP <80% OR
..(skill) Fifth DPS when HP <80%
That would at least get rid of the blowing the cool downs and tune the Fairy to the SCH's Play style better. For SMN something similar could be designed based on Players target, Tank's target.

Personally I find that being able to tune the pets would be more useful, since many people complain about the Pet AI already.