Answer 1

Put the rules on top. Make it collapsible so it would not take up too much space when not needed.

Put a start button so that the player wouldn't be pressured to play the game until he is ready.

Group the buttons closer so that there is no need to scroll.

Maybe use cute animated icons instead of words for the buttons and provide better graphical feedback when they are pressed to hold the player's attention and keep the game interesting.

For the javascript, assign variable names for your DOM elements, so you don't have to keep using document.getElementById() repeatedly inside your functions.

Answer 2

I suggest moving the if statement at line 17 to the outside function. And remove the return keyword from the if statement.

Doing this will solve the laggy countdown timer that appears inside the message box.