Colour My... Series/WMG

The stick girl awakened the protagonist's coloring powers.

In Colour My Heart, clicking doesn't color things. The only color in the game is around the girl, as the two embrace at the end. In subsequent games, however, clicking DOES color things.

The stick people were once human before whatever-it-is took over the city.

Or maybe they still are human, but they no longer see themselves as such.

In the final game of the series, the robots will finally be overthrown and the protagonist and his girlfriend will start to appear as normal humans.