I really like your game! The concept of controlling squares is strong, and it fits the control theme really well. I think this deserves more attention. It is a solid foundation for a good game that can be expanded on.
I guess a quick improvement would be to make controlled tiles more visually clear with an icon or checkmark. It was hard to tell when zoomed out.
One crazy suggestion to consider: maybe remove the timer all together. The player hits "Space" to bring the next wave, and gets money at the same time. I love the game tho, thanks for sharing.