grant,
Your itinerary seems a bit "ambitious" for such a short time frame, although it's certainly feasible. Visiting six locations in 16 days is an average of 2.6 days in each location, with no allowances for travel times. You'll have to decide whether you're both willing to do a "blitz" itinerary with all the travel, checking in & out of hotels, etc. and not really having time to see much in each of the places you're visiting. Don't underestimate the effect of travel days, as in some cases you'll need the better part of full day for getting from one location to another.
Using your latest Itinerary, changing the order slightly would be more efficient....
- Barcelona
- Nice
- Cinque Terre (getting to the C.T. from Nice is a relatively easy trip, about 5-6 hours or so by train - usually one change at Ventimiglia and sometimes more depending on which trains you choose - in this case, keeping the C.T. in the Itinerary makes sense - which of the five towns are you planning to stay in?).
- Venice
- Siena - for travel to Venice to Siena, the easiest method IMO would be high speed train from Venice to Florence (2H:05M) and then Bus from Florence to Siena (about an hour via Corse Rapide Bus). The advantage of Bus is that you'll be dropped right in town, rather than at the bottom of the hill where the rail station is located).
- Rome
Of all the locations, Barcelona seems like the "outlier" in this case so dropping it would make the rest of the trip a bit more relaxed. As the guru often says "assume you will return". Starting in Nice shouldn't be a huge problem, as you can use a connecting flight from whichever European gateway you use.
Your home location wasn't listed in your Profile, so I assume you're travelling from North America? If that's the case, you'll generally arrive in Europe the day after you leave, and the last day will be required for the flight home.
One final point to mention is that if you haven't travelled by train in Italy, there are some potentially expensive caveats to be aware of. If you need more information on those, post another note.
There are lots of possible ways or arranging your Itinerary, and this is only one suggestion.
Congratulations to both of you and happy travels!