Just one word: tombstone. Always try to fight with boss near tombstones. It gives you exp 5x faster(but only if you will hit all tombstones, and its hard). Even standing behind lazer attack wont give you that big exp number...
I wonder if my enemy did not try to increase his(her? it?) income. Enemy only built war buildings. And so he did not have enough money to get upgraded units, general and more units in army.
You know what will be the best? Do your game like in dungeon keeper. Its strategy, but you can choose one of your soldiers and play as him/her. Do it here, you made both engines(strategy, shooter), connect them please!
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