The reason why Macedonia vs. Grece, unlike China vs. Mongolia, are not represented as distinct civs is just a limitation of a narrow game design. But these gross simplifications of Firaxis's shouldn't misled us into thinking that Alexander's empire "makes more sense as a Greek civilization than a Macedonian one". Anyway, my original argument was that Greek mainland, under Philip and Alexanders rule, was more like conquered land than a cohesive and independent state. So I think that to regard Alexander's Grece as a truly unified nation is dubious to say the least. It seems to me that this argument still stands regardless of you comparison with of Macedonia/Greece with China/Mongolia, unless I've somehow missed the point of your comparison.
Actually, I'd love to see Al-Andalus in the game. I guess that people would object on the grounds that it "overalps" with Spain, or that it should be represented by a generic Arab civilization. The real problem as I see it is that Civ4 (and probably Civ5 too) doesnt really allow fragmentation of lager empires (Civ4s Vassal States didnt really succeed in simulating that properly, but I hope that Civ5s Puppet States and City States will be somewhat better).The Moors and the Berbers certainly deserve to be in the game as a major civilization: Al-Andalus could then spawn as a fragment of the Moors.
Although I do happen to think that Italy roughly falls into the same European league as Spain, France or Germany, I am not in the business of arguing that country X is more influential than Y. These argument are often silly, and I have no interest in getting bogged down in these kind of comparisons. In fact, I don't even think that some other civ should be excluded in order to make room for Italy.
Rather, I am for increasing the total number of civs and introducing a more dynamic game mechanics whereby ancient cultures rise, collapse and get gradually replaced by their modern counter-parts. With a system like that in place, Italy may emerge later in the game as the closest continuer of ancient Rome.