It's quite simply down to the restriction of the number of factions we can have in game (damn CAs hard coded limits).

Whilst many modding tasks have been boosted, they have overlooked some key areas, sigh.

But with Italy, it doesn't matter what route we take, people will complain, if we just choose one of the major states over all others, some will say 'city/region X was more important', and by taking the unified italy route, we get people saying its ahistorical.
We know that, but at this point in time, its the best solution we can come up with. If you want it changed, pester CA to give us a greater number of faction 'slots' ingame, as it stands, there is nothing else we can really do.