One major issue is one of headspace, as you sacrifice a day of holiday for a day of travel. You have to feel on holiday right as you enter the train. If you're getting antsy for every hour not spend at your destination, you will never be happy with anything but flying. But we had a wonderful time on the ferry and waiting for our connecting trains, we had a nice time in both Newcastle and Amsterdam.
With a toddler in tow, the freedom of movement and the space in a train or on a ferry beats air travel or car travel almost every time.
For next year we plan on spending even more time "travelling". Adding one or two additional overnight stops between rail connections is fine with us. It's fewer days at the destination and it's a bit more expensive with the multi-leg train journeys. But as the travel is not very stressful that way, it comes out about even.