We have just got back from a week travelling between Switzerland (where we live) and Italy by train - Geneva to Milan, Florence and a stop on Lake Maggiore on the way back. Last summer my middle child and I went from Amsterdam vis Hamburg (definitely one to avoid), Copenhagen and back to Amsterdam and DH took all three to England, flew in to Edinburgh, train to Durham, London, Exeter and flew back out of Bristol, interail was cheaper than booking on normal routes, this is not always the case.
This year, Germany are offering unlimited travel on local trains for 26 euros for a month so worth looking at if you want to see other parts of Germany, you can travel all over the country as long as you avoid the InterCity (IC) trains.
When we were booking last year, we were too late for the overnight from Amsterdam to Berlin so do make sure you have your reservations in place. You can book these through the Interail site but there was some that were unavailable there but it was possible to book them on the sites for the train operators by country instead. We were able to change some journey plans while we were travelling but not others. Germany was particularly busy last year, possibly due to the 9 euro travel offer but maybe it is always busy. The train was packed between Hamburg and Copenhagen with many people standing the whole way, we were very grateful for our compulsory reservations.
We use a mixture of hostels and airbnb's. With 5 of us, airbnb's usually work out cheaper. Having cooking facilities is important for us as we don't eat gluten do breakfast and lunch are tricky on the go.. so we prefer to be flexible and this week we packed our own lunches in food flasks for the journey days. While I have been tempted to book accommodation close to the train station, this is not always the best option as the areas around train stations can be pretty grotty whereas hopping on a local train for 15 minutes, might take you to a much nicer area, but that is difficult to know in advance. Hostels usually have good places to hang out and be around other people whereas airbnb's might be quite funky locations and give you your own space and leisurely use of the bathroom. We pack quite a few games for the train, waiting in restaurants and hanging out in the evening.
If you have your heart set on particular museums or attractions, it is a good idea to book them in advance. The world is busier than it was when I travelled Europe in 1995! We have rocked up at museums only to find there were no tickets available for the next three days. Even with timed tickets, you might have to queue for quite a while - we experienced this in Italy this week, I can only imagine how busy it gets in the summer. Early mornings seem much better than 11am onwards. There are many ticket resellers which makes getting tickets more complicated. I have yet to see the advantage of the city tickets offering museum entry but getting city transport tickets is usually a good idea - can be complicated with kids as much of it is on apps these days which can be a challenge with urban transport - but there is always a solution!
We still enjoy the type of walking routes from darling Kindersley and Lonely planet guides which tell you a little about the area and take you to less famous attractions. We got our fix of churches in Florence from walking around the outside of the one with the enormous queues and popping into other less popular ones instead! Though obviously, the big famous ones are busy for a reason - just sometimes it's nice to find other things. We are also big fans of browsing a flea market!
Don't believe everything you read and do read reviews!! There will be things that don't quite work - that is all part of the journey.