I totally agree with eviator's quote from your Gameplay page. To me one of the biggest differences will be what buffs/bonuses each unit brings to the whole and to specific units.
Here is my take:
T1:
Hermes(scout): Adds a 1 time (non-stack-able with additional Hermes) range bonus to both brute and archer at the expense of not using its weapons while attached to groups with either of those units in them. Adds LOS in ONE direction (up to eight directions)per Hermes for every unit in the group it is attached to.
Brute: Adds a small but stack-able rate of fire bonus to the secondary energy weapons of zeus and all t3. Adds a small but stack-able engagement maneuver speed(target tracking) bonus to all other t1(except Hermes) and t2 units.
Archer: Adds a small but stack-able rate of fire bonus to Artemis. Adds a small but stack-able evasive maneuvers speed bonus to all other t1 and t2 units.
Energizer: I think it is fine as it is unless given further research and/or upgrades for more abilities.
T2:
Artemis: Adds a small but stack-able area of effect bonus to Archer, adds a small but stack-able penetration bonus to all energy tier units firing on the same target as any Artemis(s) that is in the same group. And adds a small but stack-able rate of fire bonus to Centaur.
Apollo: Adds a small but stack-able accuracy bonus to any unit adjacent to it and adds a small but stack-able anti-air accuracy for any unit capable of firing on air units.
Nemesis: Adds a small but stack-able penetration bonus to Brutes, Zeus, Hercules, and Prometheus adds a stack-able range bonus to the secondary weapons of all t3 units and a moderate but non-stack-able damage bonus to all Archers and Artemises within the same group and firing at the same target.
Zeus: Adds a small but stack-able damage bonus to brutes and to the secondary energy weapons of all tier 3 units. Adds a small but stack-able anti-penetration bonus to all other t1 and t2 units.
T3:
Hercules: 1st off I think that the primary weapon quality of Hercules and Prometheus should be reversed in your chart Frogboy(unless that is, the names in our game version that we have is backwards.) It seems to me that Hercules would have a higher penetration, higher range weapon than Prometheus, and that Prometheus would have a higher dps or rate of fire. At any rate: Adds moderately high damage bonus to nemesis and moderate damage and small penetration bonus to brutes and Zeus. By default will always protect Archers, Artemises and Apollos first, unless manually selected to do something otherwise. Anti T3, repair function, target priority selection, or anti-air screen could be good secondary abilities.
Centaur: Adds moderately high range bonus to both Archers and Artemis. Adds moderate penetration and small damage bonuses to all other t2 and t1 main weapon. By default, tries to assist Hermes, Brutes and Zeus first.
Prometheus: Adds moderate rate of fire bonus to Brute, Zeus and Nemesis adds moderate armor to All units. (this one might be too much?). If 20% or more of meta-unit consists of Nemesis, Prometheus will protect them, otherwise Prometheus supports all units equally as it looks to me in the game to be a medium range unit, also both Brutes and Zues will rally with Prometheus
It seems to me that a good rule of thumb should be that if a meta-unit consists of less than 50% of Brutes and/or Zeus, that they should hang back and protect the longer range units. (The only exception being if Prometheus is the T3 in the unit). With +50% of brawlers though, they would rush to attack the enemy and leave a gap between them and the more ranged units.
Thank you Frogboy for starting this thread and allowing us to contribute. What I suggested, is obviously in no way perfect, or maybe even applicable. But I think something like these shared bonuses would allow each meta unit to have its own set of advantages and disadvantages. To me this is part of the intimacy or customization aspect that could make each army and thereby player unique in a sense.
And we have not talked about meta-unit size limit, if there is one and if more than one T3 unit may be assigned to it.
I hope this adds something of value to the topic of this thread.
thanks.