I have the feeling that Assassin's Creed II made Florence and Venice so famous that most casual players won't be too surprised if the see either of them as the Italian capitol.)
Oh yes!
No, that's far too much of a stretch. I don't dispute your point about those cities' relevance as being inaccurate, but you're looking at it from too in-depth of a perspective. Look at it from the point of view of casual fans, all the people who play this game and don't check fansites or have an extensive knowledge of history; the vast majority of people who would buy this expansion would look at Italy, see Firenze/Venecia, and immediately question why the capital of Italy isn't Rome.
I'm not saying your overall point is invalid, or that Italy wouldn't be a good addition (I'd like it, personally), but Rome must be its capital.
It's no problem to assume that's what they'll do. Siam's city list doesn't even include Bangkok/Krung Thep and has Ayutthaya near the end of their list, in addition to including multiple cities that are no longer Thai (Vientiane, Luang Prabang)
You have no idea how surprised I was at Siam's city list. Ridiculously in-depth.