The biggest problem of this game is the lag when there are more that 100 units. I've tried EVERITHING to fix this as a player. JNI should really put 60% of his huge efforts in fixing this problem. Maybe switch to another engine would help. I'm not sure how this kind of stuff works. Apart from that, this game is really good. A must try if you enjoy indie games.
That's the problem of your computer. Since the last update, I can play with about 300 units on my computer. I haven't created the game for extremly large battles with thousands of units. There are other things in the game like the destruction, dismemberment and player controls.
Btw you can't just change the engine if you want to. You would have to restart the development if you change the engine.