I played in full-screened and had a great time, but I thought that if the game remained embedded within the page, the gaming area would be too small to play comfortably. For example, the upgrade selection menu extended beyond the game area. I think scaling the entire screen to match the game area size would help maintain a consistent level of difficulty and gameplay experience.
Also, when I was engrossed in playing with the mouse, I'd accidentally click when the upgrade screen popped up and end up proceeding without realizing what I'd selected. I think adding a brief pause when the upgrade screen appears would improve the gameplay experience, too.
Anyway, it was so much fun that I kept playing until I beat the game. 🙂