Is her expert pilot ability only for taking Viper related actions or can it be any two actions?

For example, during one turn in our first game, the Starbuck player started the turn in a viper. During the movement step, the player discarded a skill card to return to the Research Lab on the Galactica. Her first action was to use the location to draw an Engineering card. Her second action was to play Executive Order giving another player two actions.

This worked out very well for the humans, but the cylon player was not happy.

Strictly speaking not - it has been commented upon before,

As your Cylon player no doubt noted, it doesn't seem very in character - but it does make the ability useful,