I had a similar problem. The moment you started making the opponents good, you had more problems to deal with and more work required to balance things. Maybe just give the better AI to certain units or just for the allies. But post jam, you have a lot of freedom to improve on this in a better way.
In a lot of ways this helped drive home a bunch of ideas on game design.
One idea that I've had after the fact would be to have parts of the enemy army trigger individually (effectively "cheating") - I definitely didn't have time to work that one out during the game. The current version of the AI uses the same controls as the player.
I really do want to keep iterating on some of the ideas in the game (either as later post-Jam iterations or in future games)
By the way - thanks for the feedback!