Tuscany is good Early game, Italy is much better once you get some steam going, and have conquered the Italian Penisula + outlying area.
Exactly. The two fit each other like foot and shoe.
For instance Tuscany's +1 Papal Influence is great early on when you are small, but as you grow you want more projection. The same can be said about the Merc cost reduction, great early on, much less important when you get the income flowing. Even more so with the interest. You are not likely to get loans when you have all of Italy, but as Tuscany they can save your bacon. The Prestige is good early on when you are less able to farm Prestige in war (there isn't much Prestige in beating an OPM with 5k troops), and obviously it is much less important when you can better decide upon your own wars.
Tuscany's ideas are damn awesome for an up and coming small state, but a lot of the greatness falls away as you grow in power. And that's where Italy comes in. Once you have Italy covered you are no longer easily able to expand using vassal-annex (it is quite easy in Italy). By then you need to forge claims and often core stuff yourself. So obviously the coring bonus is a significant boon. The Galley bonuses are perhaps not great, but they are clearly designed to let you take control of the Med, and they are better than most others' around you. The IA bonus is just great, nothing much needs to be said about it. The infantry power bonus is not exactly as good as the discipline, so that's a loss. But you gain in both trade power and tax income, very much welcome. The BROT bonus is good right now, and should become absolutely wild in 1.5. You gain in manpower, which is always good. You exchange the tech and idea discount for stability cost reduction, that one depends, but often it isn't overall MP you need, but ADM. Along with the coring bonus you should be pretty safe here. Production versus defensiveness, yeah that's not so great, but not everything can be a clearcut win or a marginal loss. But even so, production is generally not the most powerful way of income anyway, while defensiveness can really help in a multiple front war, besides defensiveness is not worth a lot when you are small and they besiege a third of your country just by moving in. It is much better the bigger you are letting you have time to raise new forces or recall from other fronts.