Wildfire could become the "communio". In two ways possible, either put it on a "Confiteor" to conclude the phase.
Either as a Primal Rend, making Hypercharge 3 stacks to be used with heatblast, but Hypercharge also giving the primal rend buff.
Visually, I'd like if a single Target Auto cross bow could be used instead of the gun that spews.. Fireballs.

I'm glad we agree that Flamethrower and AQ are terrible designs. In a future expansion, I wish Flamethrower would be another Hypercharge phase but with a 1 min cooldown.
As for the Automaton Queen, reworking it into a Phoenix/Bahamut that updates buttons would be cool.

In the end MCH would become a job that swaps between different phases like SMN, but while keeping the many tools that are on GCDs. Drill, Air Anchor, Chainsaw.
It wouldn't actually change much, it would simply replace most Hypercharge phases with something more interesting.