Travellers need to be aware that most long-distance Intercity (IC) trains which transit through Florence NO LONGER STOP at the main S.M. Novella Station, but rather at the outlying Rifredi or Campo di Marte Stations, which require a regionale train connection to reach S.M. Novella.
This also means that travellers needing to connect in Florence to other trains may face a similar need to connect to (or from) S.M. Novella Station.
For example, if you are taking the IC train from Venice to Florence to connect to Arezzo, Cortona, Perugia, Assisi, Spello or Foligno, you won't be connecting in Florence at all, but in Arezzo. If you want to get to Naples (or Chiusi or Orvieto) from Florence on the IC train, you'll have to take a regionale train to Rifredi Station to board the IC. And only two of the seven IC trains between Rome and Florence go into S.M. Novella Station (the other five stop only at Rifredi).
By contrast, if you're connecting from the IC train to a regionale train to Viareggio, Lucca, Montecatini, or Pistoia, you can connect at Prato Centrale. If you're going to Pisa, connect at Firenze Rifredi.
So, BEWARE when travelling on any IC train to, from or connecting in Florence. Check the Trenitalia schedules to verify whether your particular IC train goes into S.M. Novella Station. If you're connecting, determine your correct connection station.
The reason that most IC trains skip over S.M. Novella Station is to save time: to reach this station requires branching to a dead-end line, whereas the Rifredi/Campo di Marte stations are on the main through line going from north to south. Hence, IC trains originating in Milan or Venice (southbound) or in Naples or Rome (northbound) stop at Rifredi on the main line and not at S.M. Novella on the dead-end line.
Eurostar (ES) and AV trains continue to stop at S.M. Novella Station.