Padua - day trip from Venice or on the way to Siena?

It works either way but there are pros and cons. Pros: If you do Padua as a day trip from Venice, it's a 26 minute train ride each way, you don't have to be overly conscious of time and you don't have to deal with luggage. With some planning you can use the much less expensive Regional Veloce trains that are just as fast as the Freccia. Cons: If you stop in Padua on the way to Siena, you'll need an extra train ticket and you'll need to check your luggage at the station. If you plan to pre-purchase your Venice to Siena tickets to save on the high-speed trains fares, then you'll be locked into a departure time from Padua. Weigh the pros and cons and decide which option works best for you.

I agree - a day trip to Padova will give you much more flexibility. Scrovengi tickets are time specific and they don't give you that much time inside. What I've done in the past was book that as the first and last stop of the day (yes, 2 visits!). In between times you have plenty to see by foot, by bus, by tram.

The trip to Siena offers a couple possibilities. You can train it all the way with change in Florence. The local train there drops you at a fairly inconvenient place in Siena. Of course, that depends on where you are staying. I prefer taking the bus from Florence. It lets you off very close to the medieval city. Depending on where you are staying, again, it might be an easy walk. The bus is much more scenic, by the way.

Look like a day trip from Venice is the way to go.
And I've definitely gotten the message from multiple sources that switching from train to bus in Florence is preferable. Thanks.