Unicode kind of does this already with dotless 'i'; capital 'ı' and lowercase 'İ' are represented as regular latin 'I' and 'i' respectively, despite being semantically different letters.
hungarian "a" is also a separate letter from hungarian "á" but shares the same glyph with english "a" (edit: all vowels are actually considered different letters in their accented form in hungarian, while obviously they are the same letter with a modifier in some latin languages).
