AWESOME GAME! but ARGH! the trading..
The most annoying thing in this game though is the darn trading, I can see that you tried to combat this by allowing us to hold down the mouse button instead of just spamming. However that just won't cut it when you need to trade on such a gigantic scale to get certain upgrades or buildings completed why can't you trade in bulk? As others have stated I needed to spend countless minutes just waiting to trade enough resources just to buy the gold/silver I needed to spend another few minutes trading that for the resources I need.
The random events, though there cool are a bit too minor after the mid point of the game. I will admit though I probably didn't encounter all of them so I'll hold back on most of my judgement in regards to score. (I never did get to see a necromancy invasion)
A feature that I almost missed was the EXP, at first I thought it was pointless.. that is until I restarted the game, where my exp was converted into resources. Which made me smile since I was able to easily get back into the game, and not only that I was able to get resources which I was struggling to get during my first play though
Having your heroes leadership being affected by their training and environment is a genius trait that I've almost never seen on a flash game. This is something that I only see in retail RPG/Strategy games. Which also brings up a point. There should be quests where numbers and pure strength/luck shouldn't mean everything. There should also be missions that require stealth and/or specialized squadrons to get the job done and you can't rely on brute force alone to accomplish.
I know I got other suggestions on the brain.. but I can't put my finger on them.. I'll probably PM them later when I play through the game some more.
For a simple practice project for your programming, you have actually invented an extremely unique flash game here. I can't wait to see where you will take it.