The controls, but this is mainly a problem for lefties. There's no option to change the settings, and it doesn't support the Circle Pad Pro, making the game even more difficult than it needs to be. This has been addressed in the sequel, thankfully.
The "savings" mechanic causes the player to more often then not be unable to afford any towers on the first day.
The map is extremely small and the icons cannot be touched to see the health of a tower unless the player goes to another menu.