We are having our honeymoon in late Sept2012 , and we have most of our trip planned. There is a leg of our trip where we are staying in CT(Vernazza) for two nights, and then going to Rome for 3 nights. We are taking the train and are looking for a location to stay the night between these areas. We like to avoid touristy things, but when in Rome.... any suggestions or preferences?
I would suggest that Lucca would be a far better choice than Pisa. There's not much in Pisa other than the leaning tower. But, you don't really have to if you don't need to. The train run from Vernazza to Rome takes 5.25hrs - 6.0hrs with a few as one train change. The route goes down the western part of Italy. Or, you can go through Florence if you want.
We spent a night in Lucca when traveling from Florence to the Cinque Terre and quite enjoyed it. On the other hand, you might want to consider staying in a Tuscan hill town, since it doesn't appear you are planning any time there. And yes, Lucca is in Tuscany, but very different than a hill town.
Any recommendations on a hill town? I do not want to divert to far from my next stop on my trip, Rome.
Since you are traveling by train it should be somewhere easy to reach. Orvieto might be a good choice. It is in Umbria, not Tuscany, but is a great town and only about an hour by train from Rome.
I'd highly recommend Orvieto! It's a beautiful hill town with fantastic wine, history, architecture and a wonderful cathedral. Plenty to experience for an overnight stop.