All the letters were for consonants, which is reasonable for Semitic languages like Phoenician, Hebrew, Arabic, and even Egyptian. Even aleph and ayin actually represent the glottal sounds that preceded the A's. Greek (and most other languages) desperately need to represent vowels as well, so they took a few of the consonants they didn't need, and turned them into vowels -- aleph being the obvious example. They then added a few symbols of their own to represent extra sounds they needed. Three unused letters were retained in the Greek numbering system.