The other problem you would have is size. A 3DS or WiiU screen is rectangular and somewhat small so it would be hard to draw at that level.
If a skill tree like what is used in League of Legends-- where you gain more points at each level,there are way more spaces than points, multiple trees, and skills building off one another-- you could create a system where each player can customize toward their play style. You could have tree be for chalklings, one for defensive lines, and one for general things such as cooldown and lines of vigor. This would allow for both personal customization and multiple play styles. Also, you could maybe use the touch screen to place items on your general defensive circle, an x could be used to mark bind points and tapped to place something on it.