I think the navigation is great the way it is, other than not being able to spin around the cube like crazy. I'll admit I was never good at Sudoku, so I appreciate the Beginner mode to ease players in. Nonetheless, I found it a little weird that Normal mode was locked from the start since you'd expect that to be the "normal playing experience".
Couldn't find any bugs and it was running really smooth. Hope your release goes well, it seems like a game that could get popular. Are you only releasing for Steam or also mobile later on? The GUI controls seem like they would transfer well.