Florence, all buses let you off over close to the academy. We were on our own private bus, but we were following the disney excurions. Our tour guide was saying that all busses must drop you off at one point, and then they can only pick you up at a point completely across the city. They pick up down the street from the Ponte Vecchio. It is quite a walk between the two. Do not buy tickets to any museum in florence if you are doing both florence and pisa, there is not enough time to do it justice. You can see the statue of David through a window at the academy!! A huge window that gives you a perfect, straight on view of the statue. Having gone into the museum on this visit, with such a time crunch, it was just not worth it!! And forget trying to do the uffizi, there is so much to see within the city that save the museums for another visit!!! I had no idea there was a window prior to getting there either!! So thought I would share that tidbit with all....
On Rome, I would not make any reservatons for the collesium. If you go across and down the street about a block from the collesium entrance, probably even less, you can buy tickets to get into palatine hill, and these tickets are good for the collesium as well. We did not do palatine hill, just bought our tickets for the collesium there!!! Saves tons of time, and then you are not stuck with a time slot...trust me, you will be happy to have as few time slots as possible. There are so many variables that can impact your tour that you will want the flexibility!!! And we did not wait in line at all doing this!! There are also food vendors there that have great food to eat, and it saves a lot of time!!
On the vatican, for a group tour anyway, and i think on an individual basis as well, they will only let you in at 9:30 or 10:30 booking directly through the vatican. Do not book a 9:30 tour, if you are late they will not let you in!!! And that time slot is cutting it very close!!! If you book through the bishops office for american visitors, they offer many more options, and the guide was absolutely wonderful. We had a 1:00 time slot, walked into where the group sales were and avoided a line that wrapped around the walls of the vatican. I could not believe the lines!! Anyway, they have a couple different options, museum and St. Peters Basilica, the gardens and St. Peters, etc. The cost includes admission into all of the above! And we did get to see the Sistine Chapel. Anyway, our guide also took us down below to see the burial sites of the popes. I think that was the highlight of our vatican tour for many in our group.
http://www.pnac.org/general/visiting_vatican.htm
I was not able to get reservations through the vatican, but was able to get reservations through this office.
There is also a scavi tour that they talk about on this site, and from what i hear, this is wonderful!!! Hope this helps....