This is an idea which has come up before, and now I've thought up what may be a pretty good mechanism for dealing with it. One of the problems with the random forces generator is that it creates very sloppy looking units. For the military factions at least, it would be better if there were more cohesion- a certain number of basic troops, one or two support units, and a commander. I've come up with a simple idea which should achieve this.
Let's say that a proper military unit is composed of 2 to 6 identical troopers, 0 to 2 support units, and 0 to 1 commanders. Let's further say that there are a certain number of unit types- say General, Assault, Defense, and Recon. Certain mecha will be assigned roles referenced against factions. For instance, Mecha X might be a trooper unit in one faction but a support unit in another. A mecha might also be given several different roles: the Zero Savin will probably be used as both a trooper mecha and a command mecha by the Silver Knights, showing up in its command role earlier in the campaign.
Here's how the generation will work: At the start, attempt to create a unit. The unit type will be listed in the team definition in the encounter; if undefined, General will be assumed. Each trooper will be alloted 20 points of Strength (measure of relative cost; most encounters have 100 points), each support unit 25 or 30, and each command unit 25 or so. Check to see which mecha of each type can be afforded and buy one. Each of these unit mecha will be generated at the standard skill level, except for the Commander who gets an automatic skill boost. After generating the unit (or units- very large encounters may be able to afford several), any leftover points go into random mecha as per the original generation rules.
Some factions are irregular- they don't use units like this, or don't stick strictly to the outline. The Pro Duelist Association, for instance, will never feature units of identical mecha.
Not all the mecha assigned to a faction need be given a role. In fact, this may work better if they aren't. Such designs would then represent mecha which are technically available to the faction in question but don't see much use anymore. They would still appear being used by major NPCs or as "extras", but would be less common than before.
One good side effect of this should be that fewer low-level mecha are generated in high-level encounters. I've noticed that even near the endgame, most combats feature a whole lot of Ice Winds and Buru Burus.
Thoughts?