I think the teacher chose this because its what has been used for centuries, that is what is found in music books sold in the music stores, and not because it is easy or intuitive.
A writing system must be consistent and effective, that doesn't mean that it has to be intuitive (in fact, it usually can not): is the written latin alphabet an intuitive writing system? Certainly not - in fact, writings based on ideograms like Chinese, while considered complex and unintuitive to "us" latin-writing people, are conceptually more intuitive.
Music is a very complex language, and the traditional staff notation is a convention that has been developed, evolved and tested along centuries. It's not immediate, nor easy, but is ironically more intuitive than latin characters: the horizontal position shows progress in time (usually in a consistent way, as longer notes have wider margins after them), the vertical position indicates the pitch.
It is probably not the "best" system, but I doubt there would be just one.
Take for instance the "piano roll" visualization in many music production programs (this is museScore):
This is clearly more intuitive than staff notation, as the pitch is pretty clear and time positioning is consistent, but it has its flaws: it requires a lot of space, you can easily be "lost", and using the chromatic scale can be confusing since we normally use a tonal system.
That said, also considering the spoken/written handicaps, the first thing to keep in mind is to use the music as it should: by listening and performing.
Before approaching the reading part, there are more important aspects that should be explored and understood first: pitch, time, dynamic.
Assuming that the pupil is able to vocalize in some way, that should be probably done through singing and imitation - exactly as we all do when learning to speak.
Start with short, easy melodies (if he already knows some, use them) with very few notes - avoid tunes that use an extension greater than a fourth or a fifth at the beginning.
Even a simple
C, D, E, -, E, D, C, -.
Try to do them at different heights, even very different, so that he can begin to understand the difference of listening and singing/playing very high or very low notes. Imitation can be done with your singing, and then when playing and singing: sing a simple 3-4 notes tune, try to sing them together, then sing the same tune while playing, let him try the same, then do the same tune starting from a different note on the piano.
Then there's the matter of time, both as speed and duration. You can use the same simple tune and sing/play at different speeds, or at the same speed but with shorter and longer notes.
Finally, as the above, but with different dynamics.
You can also do this while "silently" beginning to use the color method Aaron proposed, which is a very good suggestion and is actually widely used for any child. Just put those stickers on the piano, doesn't matter if you don't use them from the beginning; you can
After some time, you can put those stickers on paper, and try to show the correlation while playing.
Let him try to create its own tunes by giving him stickers to put on paper, or, even better, drawing with pastels or colored pencils. This is very important, because it allows a better awareness of what is happening and what can be possibly done.
Consider that once the basic concepts have been grasped, you can also try to play short tunes and see if he's able to "write" them down using colors (maybe you can do the opposite too: he plays some notes, and you draw them).