i think the problem is that you clearly have different stats for the enemies than the player, even though both are using "the same" units. a rock-paper-scissors style system dosent really work when the elements function differently for each side.
They all start with the same base stats, but the enemies have certain number of upgrades unlocked, so their hp, damage etc get scaled as well. However since the upgrade path the player takes may not be same as the enemy, they end up being different feeling. I will work on trying to figure out a more elegant solution!