I'm new to Sudoku, so I'm not sure how it would typically be scored, but the way this game does it is silly. When you play a tile, the name of the tile is multiplied by a number which decreases as the timer counts up. This scoring system allows for a user to be presented with the "same" board as another, execute the exact same sequence of moves with the same timing, and come to a different score. To do this, all you must do is permute all of the tile names, i.e., replace all 1s with 9s, all 2s with 1s, all 3s with 2s and so on. This doesn't really change the board since you could replace the numbers with letters or glyphs and the structure of the soduko board remains the same - there is still one one of each type of tile in each row, column, and square.
For a perfectionist like myself, this scoring system causes me to constantly restart games until I get that perfect start that allows me to play a bunch of 9s in the beginning. Ideally, the tiles would count evenly, since it doesn't really matter which tiles you are playing. If you are playing tiles at all then you're making progress. My suggestion would be to instead measure how sparse the board is (since play is more difficult the fewer tiles on the board) and multiply this value by the value determined by the timer. There are of course other options. I just don't like the way it is done now.
Other than that, SudokuMasterEdition is awesome. 4/5