I have been to all the cities you mention and many more in Europe, within the last 5 years, and I always used public transportation between cities or from the airport to the city. On every occasion I have traveled with a carry on size rolling luggage and never had an issue. Granted I have never had to get into public transport with luggage during peak commute time. Maybe I have been lucky that way. But if it is peak commute time, I am not sure if a roller duffel or a backpack would make a difference.

In both Dublin and Paris, I took an airport bus into the city and walked to the hotel, so there were no commuters per say. In Rome I took the train from the airport to the city and then the metro. In Amsterdam, which was just a few weeks ago, I took the train from the airport and then then tram from the central station to the hotel.

Talking about a traveling in a crowded train, I was in Brussels last month, and did a day trip to Bruges on a Saturday morning. I was stunned at how jam packed the train was, given that it was the weekend. It was all tourists, and many many with large luggage. So I guess it is hard to predict when a train can be crowded.