The damage amounts on the AoEs seem to be balanced for hitting all 3 pets. Ie, Punch does 20 damage; Arcane Explosion deals 10 frontline/6 backline for 22 total when all 3 pets are still alive; Tidal Wave/Lava Wave deal 7 front/7 back for 21 total. Flux is 12 front/9 back for 30 total, with a 3 round cooldown, and Whirlwind is 11 front/11 back for 33 total, both with 3 round cooldowns, making them pretty comparable to nukes like Conflag/Maul. But as soon as an opposing pet dies, the damage output plummets.
You could try something gimmicky, like Lil XT (Heartbreaker+Tympanic Tantrum is a total of 72 front/36 back over 4 turns), or Uncanny Luck + Cyclone (85% chance for 7 damage, per pet per turn, but it's a lot of swapping and Lightning Storm+Cyclone is just annoying).
Also, this is ignoring the fact that Sandstorm is common and completely shuts down any AoE strategy.