Idea for a quirk system:
A quirk is an aspect that reflects an agenda separate from the player's. Orders given to a companion will be obeyed only as long as they are in accordance with this aspect. Quirky companions get +X refresh, where X is the number of stunts invested in them.
Idea for a companion mob:
There is an upgrade stunt that copies a companion, giving you another one with the same stats. It must be applied before all other upgrades. But when you upgrade one, you can upgrade the others at half price.
Idea for limits on skill boosters:
You can only buy a skill pyramid booster after buying a refresh upgrade. You can only buy a second after taking a quirk and 4 refresh upgrades.
Okay, I just came up with those in 15 minutes. They're probably awful. Pull them apart.
I like the idea of quirks for companions, and I'd go so far as to expand the quirks beyond agendas and goals to pretty much anything that could complicate the relationship between the character and his companion, or effect the companions utility in a significant way. Assuming that companions cannot recieve Fate points of their own, this provides a good reason to create compellable aspects for the companions. I would, however, include the option for this as an part of the Companion stunt rather than as a separate system.
For mobs of companions, unless we're talking about a set of named 'Bodyguard' NPC's (which I agree would have to be seperately statted out), I think that creating them as a disposable "summonable" horde of minion level characters would be easiest.
I'm currently writing from work so don't have access to the DFRPG books, but IIRC minions simply get one/a set (can't remember which) of broad pseudo-skills for the Physical, Mental and Social spheres, and what that skill can be used for is dictated by their concept aspect (ie. mobs of reanimated zombies and loyal ninjas would likely both have a relatively high Physical 'skill', but the direction to which that could be put would be dictated primarily by their concept aspect - Ninjas being stealthy subtle agents of carnage might be able to pick a lock or stealthily steal an unguarded item, zombies being...not so subtle would probably not). This would seem to be as much as a set of player controlled minions would need skillwise.
I'd probably create it as a stunt (costing would probably need to be more than 1 refresh though due to the insane amount of variability that minions could give) that adds the 'Minions' trapping to a relevant skill (Resources for paid Mercs, a social skill (or possibly conviction) for fanatical zealots etc.).
The trapping would allow the player to roll the relevant skill vs +0 with the number of shifts indicating the number of minions that are nearby/can be called up/magically created (with them arriving at the start of the next phase), how they arrive is pretty much immaterial/flavour, whether they are summoned from the earth, drive up in their own transportation, or fade out of nearby shadows.
I'd probably limit usage of this trapping to once per 'scene' with the possible exception of spending a fate point to 'recharge' the ability (call it an invocation of whatever aspect the character has that justifies the minions).
Similar to Companion I’d suggest allowing the spending of Refresh to give the minions powers and abilities and possibly allow the purchasing of the minion ability multiple times to justify different classifications of minions (all running on the same 'cooldown timer' though), though whether they’d share a pool of Refresh, or have to buy powers separately I don’t know.
I think that mechanically, the Minions power from Strange-Fate that I posted earlier in this thread does some similar stuff (though slightly more complicated due to the more ‘crunchy’ nature of that system), but cutting it down somewhat by removing the power tiers and varied levels of minions seems to still be workable.