The most frustrating part of the game was letting units by because I couldn't tell towers who to attack... Ghosts getting through because my magic towers ignored them in favor of Giants I had well in hand was awful...
I really enjoyed the creepy atmosphere of the early parts of the game, but the further I progressed, the more the feeling came apart. Once I had figured out they were mutant flies, the tension vanished, and it was much too early in the game.
Also, I couldn't stand the unmarked spots on the walls you needed to click. For secret stuff, sure. But anything needed to progress should be visible.