First of all, this is the best $10 I ever spent on a game. None of this is a big deal but I think adding this stuff would take that last step to perfection
1. There should be a way to clear all of the pencil marks that are flashing instead of just refilling everything that's possible (backspace maybe?). As it is I have to pick the low hanging fruit on a first pass just to minimize the amount of re-work I'd have to do if I have to hit space again, or I'm stuck right clicking on 20 different boxes.
2. The Yes/No confirmation boxes should be able to be answered with the Y or N keys instead of the mouse, specifically the one that pops up after I've just hit the space bar since my hand is already on the keyboard.
3. Shade the background behind the play area a bit more. The whiter areas in the background image makes the white numbers hard to read on cheaper LCD screens.
4. Add a help menu option to display all the nifty keyboard commands. I didn't know about hitting space to fill in all the pencil marks for a couple of days after buying the game and I just now found out I can hit the number keys to highlight that number (which is important when the number didn't exist in the original puzzle)
5. Make the fade-out when taking focus away from the game window optional. With 2 monitors I'll sometimes leave the game up on one while doing work on the other and bouncing between the two and having the game keep dimming on me is a little jarring.