I'm going to throw my own suggestions out here since everyone else is
CTRL + R = run game
CTRL + L = load last
And for the love of all that is holy, please move the tile mode hotkey from ALT to Shift, and move the Copy Key from C to S, so that you can comfortably rest your hand on S, D and F with your Pinky on shift instead of trying to mangle it onto ALT while trying to reach for E, R D, F, and C. It's very painful and not easy to do. Also moving the Place entity Key from I to W would be great since it's right where you hand would be resting anyway. Also making Insert work for as well since CE did it that way would be cool maybe.
Also making the Tab key cycle between Tile, Entity, Script and Mapdata Mode would be great so that you don't ever have to move the mouse to the upper right corner to click on options. This should make it so that you can just move the mouse where you want to place things instead of the constant back and forth to the top left of the screen. You already have to do it enough when you're grabbing tiles from the tileset.
A final option that would be nice is the ability to hold shift and type an entity ID into the numberpad to instantly make that the selected Entity ID, would be very ergonomic (if you use your right hand to type in the number on the numpad)