Well, an has retained its n throughout the changes and it has not been necessary to prefix an extra n-. It would not be sensible to change a structure like ar an eitleán to ar a n-eitleán because it would have an ambiguous meaning (“on their aeroplane” vs. “on the aeroplane”). Similar to Marcoman’s example of the importance of the hyphen.
I think an important difference is that an does not always cause eclipsis, but has multiple modes of action and different meanings, unlike i which has a single meaning. After in lost the n at some point, it was necessary (probably due to phonotactical reasons) to reproduce it before vowels. First it followed suit with other cases of “vowel eclipsis” but in the new spelling rules it was relocated where it used to be.