Very nice game; good to have a tough TD game, although you'll get better ratings if you put in an easier mode. Couple of suggestions: (1) If you have multiple wall factories, it should allow you to place multiple walls simultaneously then recharge slowly. The fast recharge means that you can't use "Next wave" without losing significant wall creation. (2) The final challenges should be "good and up" and "excellent and up"; by the time I've done everything on perfect I'm done with the game. (3) The EMP tower is too powerful; the later waves don't even make it out of the entrance gate. It would be more balanced if it just affected a single unit.
The problem is not that the Ninjas are too hard, it's that the rest of the waves are really boring while you're waiting for the ninjas. Either make the whole game easier so people can finish Brilliant quickly, or make the whole game harder so it's interesting while you finish Brilliant.
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Thanks for the suggestions!