I was thinking about it and, I'd REALLY like to play a single-player strategy campaign where I breed units in between RTS battles. But I'm not sure how the breeding could fit into a multiplayer version (it's like the problem with balancing pokemon duels when players haven't completed the single player game, including maxing the level on their dueling team). As for putting the breeding right into the RTS battle, I can't see how breeding, which is a though-requiring activity, would fit into a session where one is playing as fast as possible.
Give your players a daily opportunity to recruit randomly generated offspring from the pool of fighters. Your warriors have a collective gene pool. No micromanaging. Permadeath ensures only the strongest live to pass on their genes.
I'm going with an additional gene pool for the ruling class where you match up mates and marry off daughters to other players. Creates a more hands on breeding, but is limited in scope so as not to overwhelm