This is a great tool to help beginners learn how to play. I wonder whether you might want to say something about the scoring part being slightly different from what would usually be used online or at a go club. I agree that knowing when the game is over and how to decide which player wins are big difficulties for many beginners and I like that this stone counting scoring (old Chinese) method solves two big problems for beginners. For me a possible difficulty with this scoring method would be when the beginner learning this way goes to a go club. Here in the USA probably most go club members use casual Japanese territory scoring. Especially weaker players, would not know how this stone scoring method works and I can imagine an experienced (say 10k) player playing our beginner correcting her when she starts playing inside her own territory towards the end of the game. I wouldn't want to start people out with the most used rules but maybe have a version of your player software that could score by territory as an option for when the learner is ready to play online or at a club.
My impression is that counting stones is better for the very first games on 5x5. Filling the board is very fast there, anyway. When a beginner understands the game enough to figure out life and death properly, and start to find it tedious to fill-up the board at the end on 9x9, then it might be better to use more traditional rules.
I feel that someone who learned the game with this scoring method will have no difficulty to adjust to usual methods, anyway.
I wanted to design the web site in such a way that the visitor can start playing as soon as possible. In my original plan, I wanted to introduce Chinese scoring for 9x9. But I was maybe a bit lazy, so I left stone-count scoring for all board sizes. I will probably add Chinese scoring in the future as an option.