Split them into factions with slighter differences - factions with otherwise the same units, but with slightly different numbers thereof and effect, i.e more armour / firepower, there's a bit of a difference in what you can do there
Is it really so difficult? I'm fairly confident that it wouldn't really be as difficult as you think to include different units for a pair of sides, although production wise I reckon your probably a LOT better off, I mean reskinning or slightly remodelling a unit to resemble a similar unit in a similar faction is much easier than dealing with multi-scratch based models, especially when there are THAT many animation sequences to deal with.