I like this sorta game. Just one thing.
It's about numbers. There is no mission that you can't win by filling the screen with units, and that is generally the most effective tactic. Upgrade resources a load, and you will never be short of money, ever.
But, it's very slow to place units. Three clicks. You have to do that 40-60 times sometimes, which adds up to several minutes of very slowly placing troops. I gave up, eventually. I know I could win. I just couldn't be bothered. You should add some option to fill squares with units, so it takes less time to place units.
Next, you should have some options to do stuff during the battle. It's ok for the shorter ones, but eventually the battles get pretty blah. Things like enhancing the damage of one unit per turn, or moving any unit one in any direction. This would add more variety to the battle.
Most of the units are very similar. As such, you don't need tactics. I have several suggestions to make it matter how your units move.
1. Add a diagonal attack to the spearman. This would make it unique, and suited for flanking.
2. Let the archer go backwards as well. This would let it lure enemies into its bow.
3. Allow the defenders to form shield walls. This would be a continuous link of three- five defenders, who would only attack forwards, with enhanced defence forward and lower defence sideways.
4. Make the cavalry move two units. This would let it rush.
Then you would have to think about how each moved.
Other general refinements- add an optimum number of turns for each level. Then we could seek medals.
Have a speed up button, even faster than -animations.
Add achievements, with some in game effect. Achievements are addictive.
Loved the story, btw.
Have scenarios, with a set number of units. This would force you to use each unit differently.
With some of that, this game could be a lot more awesome.