My wife and I are just returned from our Viking River, Cities of Light Cruise, with two nights in Paris to start then river cruising across Germany via the Mosel, we boarded the Idun in Trier, the Rhine and ending on the Main, before bussing to Prague for a two night stay. Two nights in Paris is not enough, so I would recommend adding a few more days on the front end in Paris as well as at least one more night in Prague.
The ground hotels Viking picked were disappointing to me because they were modern Hiltons with no sense of being in Europe. Both included a nice breakfast and comfortable bed and modern bath. But to me there are so many great hotel choices in both Paris and Prague that would have had a more European feel.
Viking managed the logistics extremely well and the busses used for transport away from the ship were modern and clean, we had no trouble with our luggage any time during our trip.