As an idea - multi-token activation could be tied to points cost. There's no particular reason for a 150-point Sister squad to need more tokens to activate than a 150-point IG blob squad, for example. Yes, the Sisters are individually stronger, but you're also paying more to get them, which is already the balancing factor.
That was the general idea i started with, and i'm using loose tiers of points to determine how many activation tokens a unit needs to activate. However, a direct relationship, say a token per 50 or 100 points, required far more tokens per player than 6, which diluted the penalties for leaving large numbers of tokens in play on the table.
As to your example of
IG vs
SoB, it would require 3 tokens to activate all 3 50 point guard squads individually, or 2 tokens as a blob of 3 squads, while that 150 point
SoB squad would take 1 token to be activated. Guard exist in a weird place, as they are the only horde army with large numbers of small squads, rather than small numbers of large squads, and as such, they needed to be treated somewhat differently. I do agree that a large squad should be more unwieldy than a smaller squad though.
If the expectation that a 150 point
SoB squad would take 2 tokens is a result of my statement that a
SM Tactical Squad would take 2 tokens, i'm estimating that a 10-man Tactical Squad is going to cost 250-300 points base in their new form, rather than the current ~150.
When do the tokens go back in the bag, and what are the limits on how often a unit can be activated? Otherwise, I can see problems with either large unit count armies versus small unit count ones, or with ignoring some units to fast-march others to objectives or into assault range.
Every unit can be activated once per game turn, with the player whose token was drawn performing a player turn in which they can allocate dice and activate their units. If a player has models near one of their commanders, they could even activate 2 units in one player turn by using the commanders activation dice.
However, no more than 1 unit may perform a reaction per player turn. Otherwise players could just castle up with some commanders, and have several units overwatch anything that dares to be activated within their
LoS.
Once the unit's finished with its activation, any activation tokens it used are placed back in the bag, and it receives a marker that shows that it's been activated this game turn. After all units have been activated, all the activation markers are removed, and the next game turn begins the cycle over.