So I've discovered today that aggression seems to be the key to winning in Fallen Enchantress.
Basically, I tried to patiently build up my production ability, explore and find good locations for cities, build stuff to help get things rolling faster, but I got an early war declaration and my cities were all too far apart to help each other.
But when I decided to go offensive and run for the nearest enemy city, I somehow win despite the odds. Granted, with some casualties, but suddenly the tide is turning because now I have the same number of cities as my opponent and might actually be on an even footing.
My mistake, I think, was to try and train all super troops in the early game, and I didn't have enough money to cover the wages, never mind that it took forever to get them out the door and fighting. If you train very basic soldiers then sure, they may not survive one battle, but you can replace them in maybe six or seven seasons. Don't get me wrong, traits are useful but they always have an associated cost and so, you're better skipping them if you need a military right away.