Glad you liked the navigation, I did put some thought into it! But my only tester told me she's only going to use mouse -_-
As for the level system it's an interesting idea. On the one hand, that's a fun thing to track your progress and get some sense of pride and accomplishment [sic], one the other I'm terrified to know how much time I've spent on, say, Simon Tatham's puzzle collection. But I think it might be worth it if paired with either a hardcore trackers — number of turns to complete, relation to the God number, time to solve — or recreational ones, like gallery of solved puzzles or cosmetic rewards.