As a voice, someone who hasn't maxed out their mastermind yet (and has started playing recently), I give a couple of opinions.
First, tie pets bonuses to set bonuses leads to complexity and likely problems, rather than outright boosting and adjusting the base numbers of the pets overall or individually, depending on the pets given. Give them either a baseline upgrade or upgrades that get unlocked based on pet level (or enchantment given, probably easier if the highest enchantment also gives them an additional boost in survivability). Problems emerge if you plan to introduce any new enchantment sets, as you need then take into account because of single AT what set bonuses are.
Another aspect is also besides enchanting pets for ability, not just summoning them (replace the dead ones), but the ability to transport them from location A to B, and more so, engage enemies faster. As if you keep pets summoned, and move in an instance, pets usually use flat movement paths rather than use their innate jumping abilities and aggro, and cause problems to the entire team, not to mention that by the time pets arrive to fight, enemies may have been killed by all other AT's.
So my own suggestion is that you can 'store' pets into a separate transport dimension and summon them from it (it has cooldown but not long one), idea is more life luxury solution to be able to summon a pet horde instantly (but you need to have summoned all of them first, normally, and then place them into a pocket dimension). As an alternative, you can dismiss the pet and then summon all of them + enchant them (which occupies MM doing nothing else in the fight, which may get over by the time they get their horde ready).
Another is that when big AoE's are done, pets die fast as well, the mastermind himself as well, cause the bodyguard featured shared HP with the mastermind is not mitigated anyway and MM may suffer the same AoE dmg equal to the number of pets caught in the AoE. Sure, keeping pets alive and position them is MM's responsibility and part of the fantasy, but need just better tools to do so or adjust the numbers so it's not so punishing.