This is both a great and a bad idea. Bad because there are plenty of factions to choose from, and how do you choose which gets represented and which don't? Especially when you get into the whole alignment thing and suddenly you've got heroes leading villain pets around and villains leading heroic pets... It's always best to keep player options as neutral as possible. Mercenaries are generic and could easily be working for either side. A good necromancer? I suppose, but he won't get along with the Banished Pantheon and their undead. Ninjas? Sure... just not Tsoo, because they've got their own agenda. And so on.
That said...
I could see a nature/elements set based on creatures from the Devouring Earth group as player pets. Maybe reshade their textures so they're independent of that faction.
Another good possibility is the Clockwork. Because they're machines, they could be reprogrammed or otherwise influenced to serve an agenda outside the main body of Clockwork. Hell, we can all have one of those if we want one anyhow with the prestige power buff pet options.
How about Zig Prisoners? You could be their liberator and they've sworn their loyalty to you?
Another untapped resource I think would cool would be monsters. No, not giant monsters --the Halloween monsters. Zombies, ghosts, vampires... that sort of thing. It can be an undead alternative to standard necromancy.
Witches... yes, we've got witches in the Halloween monsters and witches in Croatoa, but the wonderful thing about witches is there can be multiple covens. Player witch pets would be a small coven controlled by the player character.
Same thing with werewolves... player pets are just part of a small pack. Maybe the tier 9 power could let the player turn into a werewolf kind of like how stone armor transforms player into a granite form.
There's some precedent for faeries out there with Croatoa. For pets, we could go with red caps, the little faerie prestige buff pet model, and those little glowing orbs of light (wisps?)
I've never paid much attention to the Coralax, so what's the story with them --could they be divorced from the whole of that NPC faction as a group of mutant sea monsters? Maybe with some reshading of their textures they could be repurposed into a generic creature from the black lagoon type group of pets.
And finally, I'll say it again... I brought it up several times on the old forums, but what about illusions? Illusion is the one control set dominators don't get for some reason, giving controllers a monopoly on that kind of power. Maybe bring the illusion pets into a MM set. Your buffs would just be upgrading their fearsome auras, and the set also boasts a couple of useful ranged attacks for the player to use.
That's my two cents.